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January 22, 2015 20:59
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| $ mvn clean install -P scala-2.11 | |
| [INFO] Scanning for projects... | |
| [WARNING] | |
| [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-core_2.11:jar:0.15.1-SNAPSHOT | |
| [WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.adam:adam-core_${scala.artifact.suffix}:[unknown-version], /Users/mheuer/working/fnothaft-adam/adam-core/pom.xml, line 10, column 15 | |
| [WARNING] | |
| [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-apis_2.11:jar:0.15.1-SNAPSHOT | |
| [WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.adam:adam-apis_${scala.artifact.suffix}:[unknown-version], /Users/mheuer/working/fnothaft-adam/adam-apis/pom.xml, line 11, column 15 | |
| [WARNING] | |
| [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.adam:adam-cli_2.11:jar:0.15.1-SNAPSHOT | |
| [WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.adam:adam-cli_${scala.artifact.suffix}:[unknown-version], /Users/mheuer/working/fnothaft-adam/adam-cli/pom.xml, line 11, column 15 | |
| [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] Reactor Build Order: | |
| [INFO] | |
| [INFO] ADAM | |
| [INFO] ADAM: Core | |
| [INFO] ADAM: APIs for Java | |
| [INFO] ADAM: CLI | |
| [INFO] | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Building ADAM 0.15.1-SNAPSHOT | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] | |
| [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ adam-parent --- | |
| [INFO] Deleting /Users/mheuer/working/fnothaft-adam/target | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent --- | |
| [INFO] | |
| [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent --- | |
| [INFO] Modified 0 of 298 .scala files | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:compile (scala-compile-first) @ adam-parent --- | |
| [INFO] No sources to compile | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:testCompile (scala-test-compile-first) @ adam-parent --- | |
| [INFO] No sources to compile | |
| [INFO] | |
| [INFO] >>> scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) > generate-sources @ adam-parent >>> | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent --- | |
| [INFO] | |
| [INFO] <<< scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) < generate-sources @ adam-parent <<< | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) @ adam-parent --- | |
| [INFO] No source files found | |
| [INFO] | |
| [INFO] --- maven-install-plugin:2.5.1:install (default-install) @ adam-parent --- | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/pom.xml to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-parent/0.15.1-SNAPSHOT/adam-parent-0.15.1-SNAPSHOT.pom | |
| [INFO] | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Building ADAM: Core 0.15.1-SNAPSHOT | |
| [INFO] ------------------------------------------------------------------------ | |
| Downloading: https://repo.maven.apache.org/maven2/org/scoverage/scalac-scoverage-plugin_2.11/0.99.2/scalac-scoverage-plugin_2.11-0.99.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scoverage/scalac-scoverage-plugin_2.11/0.99.2/scalac-scoverage-plugin_2.11-0.99.2.pom (4 KB at 2.6 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.pom (2 KB at 44.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.1/scala-xml_2.11-1.0.1.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.1/scala-xml_2.11-1.0.1.pom (3 KB at 79.3 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom | |
| [WARNING] Checksum validation failed, expected ./spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom: but is 563042a54b97e31af4529ea0db79ba2c4c2bb6cc for https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom | |
| [WARNING] Could not validate integrity of download from https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom: Checksum validation failed, expected ./spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom: but is 563042a54b97e31af4529ea0db79ba2c4c2bb6cc | |
| [WARNING] Checksum validation failed, expected ./spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom: but is 563042a54b97e31af4529ea0db79ba2c4c2bb6cc for https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.pom (19 KB at 216.2 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/com/twitter/chill_2.11/0.5.0/chill_2.11-0.5.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/com/twitter/chill_2.11/0.5.0/chill_2.11-0.5.0.pom (3 KB at 72.4 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom | |
| [WARNING] Checksum validation failed, expected ./spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom: but is 9658277c1948931f7b601f29ea3606e840a86abb for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom | |
| [WARNING] Could not validate integrity of download from https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom: Checksum validation failed, expected ./spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom: but is 9658277c1948931f7b601f29ea3606e840a86abb | |
| [WARNING] Checksum validation failed, expected ./spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom: but is 9658277c1948931f7b601f29ea3606e840a86abb for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.pom (4 KB at 63.3 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom | |
| [WARNING] Checksum validation failed, expected ./spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom: but is 71f4a097cd36db829ec8a0717fdd644530a60c19 for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom | |
| [WARNING] Could not validate integrity of download from https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom: Checksum validation failed, expected ./spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom: but is 71f4a097cd36db829ec8a0717fdd644530a60c19 | |
| [WARNING] Checksum validation failed, expected ./spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom: but is 71f4a097cd36db829ec8a0717fdd644530a60c19 for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.pom (4 KB at 60.0 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-remote_2.11/2.3.4-spark/akka-remote_2.11-2.3.4-spark.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-remote_2.11/2.3.4-spark/akka-remote_2.11-2.3.4-spark.pom (4 KB at 114.0 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-actor_2.11/2.3.4-spark/akka-actor_2.11-2.3.4-spark.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-actor_2.11/2.3.4-spark/akka-actor_2.11-2.3.4-spark.pom (2 KB at 61.0 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-slf4j_2.11/2.3.4-spark/akka-slf4j_2.11-2.3.4-spark.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-slf4j_2.11/2.3.4-spark/akka-slf4j_2.11-2.3.4-spark.pom (3 KB at 83.6 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/json4s/json4s-jackson_2.11/3.2.10/json4s-jackson_2.11-3.2.10.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/json4s/json4s-jackson_2.11/3.2.10/json4s-jackson_2.11-3.2.10.pom (3 KB at 66.8 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/json4s/json4s-core_2.11/3.2.10/json4s-core_2.11-3.2.10.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/json4s/json4s-core_2.11/3.2.10/json4s-core_2.11-3.2.10.pom (3 KB at 21.4 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/json4s/json4s-ast_2.11/3.2.10/json4s-ast_2.11-3.2.10.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/json4s/json4s-ast_2.11/3.2.10/json4s-ast_2.11-3.2.10.pom (2 KB at 63.4 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scalap/2.11.0/scalap-2.11.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scalap/2.11.0/scalap-2.11.0.pom (2 KB at 48.3 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.0/scala-compiler-2.11.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.0/scala-compiler-2.11.0.pom (3 KB at 76.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.0/scala-reflect-2.11.0.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.0/scala-reflect-2.11.0.pom (2 KB at 51.0 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.1/scala-parser-combinators_2.11-1.0.1.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.1/scala-parser-combinators_2.11-1.0.1.pom (3 KB at 72.6 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.11/2.2.2/scalatest_2.11-2.2.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.11/2.2.2/scalatest_2.11-2.2.2.pom (6 KB at 175.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.pom (2 KB at 52.8 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.pom (3 KB at 79.3 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scoverage/scalac-scoverage-plugin_2.11/0.99.2/scalac-scoverage-plugin_2.11-0.99.2.jar | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.1/scala-xml_2.11-1.0.1.jar | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.jar | |
| Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar | |
| Downloading: https://repo.maven.apache.org/maven2/com/twitter/chill_2.11/0.5.0/chill_2.11-0.5.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scoverage/scalac-scoverage-plugin_2.11/0.99.2/scalac-scoverage-plugin_2.11-0.99.2.jar (210 KB at 1648.4 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar | |
| [WARNING] Checksum validation failed, expected ./spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar: but is 268142918dd9ba3f391ec329839d999facc3ff42 for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.1/scala-xml_2.11-1.0.1.jar (641 KB at 2645.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar | |
| [WARNING] Could not validate integrity of download from https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar: Checksum validation failed, expected ./spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar: but is 268142918dd9ba3f391ec329839d999facc3ff42 | |
| [WARNING] Checksum validation failed, expected ./spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar: but is 268142918dd9ba3f391ec329839d999facc3ff42 for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.11/1.2.0/spark-network-common_2.11-1.2.0.jar (80 KB at 191.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-remote_2.11/2.3.4-spark/akka-remote_2.11-2.3.4-spark.jar | |
| [WARNING] Checksum validation failed, expected ./spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar: but is f43e367fe7a05e3b99e501fc7447703921dcc1c3 for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/com/twitter/chill_2.11/0.5.0/chill_2.11-0.5.0.jar (214 KB at 357.7 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-actor_2.11/2.3.4-spark/akka-actor_2.11-2.3.4-spark.jar | |
| [WARNING] Could not validate integrity of download from https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar: Checksum validation failed, expected ./spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar: but is f43e367fe7a05e3b99e501fc7447703921dcc1c3 | |
| [WARNING] Checksum validation failed, expected ./spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar: but is f43e367fe7a05e3b99e501fc7447703921dcc1c3 for https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-shuffle_2.11/1.2.0/spark-network-shuffle_2.11-1.2.0.jar (57 KB at 84.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-slf4j_2.11/2.3.4-spark/akka-slf4j_2.11-2.3.4-spark.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-slf4j_2.11/2.3.4-spark/akka-slf4j_2.11-2.3.4-spark.jar (16 KB at 21.2 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/json4s/json4s-jackson_2.11/3.2.10/json4s-jackson_2.11-3.2.10.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/json4s/json4s-jackson_2.11/3.2.10/json4s-jackson_2.11-3.2.10.jar (41 KB at 51.8 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/json4s/json4s-core_2.11/3.2.10/json4s-core_2.11-3.2.10.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-remote_2.11/2.3.4-spark/akka-remote_2.11-2.3.4-spark.jar (1312 KB at 1556.1 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/json4s/json4s-ast_2.11/3.2.10/json4s-ast_2.11-3.2.10.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/json4s/json4s-ast_2.11/3.2.10/json4s-ast_2.11-3.2.10.jar (81 KB at 89.7 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scalap/2.11.0/scalap-2.11.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scalap/2.11.0/scalap-2.11.0.jar (754 KB at 619.2 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.0/scala-compiler-2.11.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/json4s/json4s-core_2.11/3.2.10/json4s-core_2.11-3.2.10.jar (564 KB at 461.5 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.1/scala-parser-combinators_2.11-1.0.1.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.1/scala-parser-combinators_2.11-1.0.1.jar (410 KB at 276.7 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.11/2.2.2/scalatest_2.11-2.2.2.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/spark-project/akka/akka-actor_2.11/2.3.4-spark/akka-actor_2.11-2.3.4-spark.jar (2473 KB at 1465.7 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.jar | |
| [WARNING] Checksum validation failed, expected ./spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar: but is fb4a0e13540962b024f720675efee1795a4adb3a for https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.2/scala-library-2.11.2.jar (5416 KB at 2031.3 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.2/scala-reflect-2.11.2.jar (4289 KB at 1338.1 KB/sec) | |
| [WARNING] Could not validate integrity of download from https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar: Checksum validation failed, expected ./spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar: but is fb4a0e13540962b024f720675efee1795a4adb3a | |
| [WARNING] Checksum validation failed, expected ./spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar: but is fb4a0e13540962b024f720675efee1795a4adb3a for https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/1.2.0/spark-core_2.11-1.2.0.jar (6830 KB at 1714.7 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scalatest/scalatest_2.11/2.2.2/scalatest_2.11-2.2.2.jar (6987 KB at 1648.5 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.0/scala-compiler-2.11.0.jar (13336 KB at 2388.6 KB/sec) | |
| [INFO] | |
| [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ adam-core_2.11 --- | |
| [INFO] Deleting /Users/mheuer/working/fnothaft-adam/adam-core/target | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core_2.11 --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core_2.11 --- | |
| [INFO] | |
| [INFO] --- git-commit-id-plugin:2.1.9:revision (default) @ adam-core_2.11 --- | |
| [info] dotGitDirectory /Users/mheuer/working/fnothaft-adam/.git | |
| [info] git.build.user.name Michael Heuer | |
| [info] git.build.user.email heuermh@acm.org | |
| [info] git.branch split-compile | |
| [info] Tag refs [ [Ref[refs/tags/adam-parent-0.6.0=cc1d98f4cb95b63f7f4b2ab4768843cce51a3a9c]] ] | |
| [info] Resolved tag [ adam-parent-0.6.0 ] [ PersonIdent[Matt Massie, massie@cs.berkeley.edu, Sun Jan 19 12:43:54 2014 -0800] ], points at [ commit 5fe4f1cdca401bdfb036c3ce4132259abc56d019 0 ------ ] | |
| [info] key [ commit 5fe4f1cdca401bdfb036c3ce4132259abc56d019 0 ------ ], tags => [ [DatedRevTag{id=cc1d98f4cb95b63f7f4b2ab4768843cce51a3a9c, tagName='adam-parent-0.6.0', date=January 19, 2014 2:43:54 PM CST}] ] | |
| [info] Created map: [ {commit 5fe4f1cdca401bdfb036c3ce4132259abc56d019 0 ------=[adam-parent-0.6.0]} ] | |
| [info] HEAD is [ 5cc2b324c9d8860a8698296191236846996e1915 ] | |
| [info] Repo is in dirty state [ true ] | |
| [info] git.commit.id.describe adam-parent-0.6.0-721-g5cc2b32 | |
| [info] git.commit.id 5cc2b324c9d8860a8698296191236846996e1915 | |
| [info] git.commit.id.abbrev 5cc2b32 | |
| [info] git.commit.user.name Frank Austin Nothaft | |
| [info] git.commit.user.email fnothaft@alumni.stanford.edu | |
| [info] git.commit.message.full Added additional fixes to get 2.11 compiling. | |
| [info] git.commit.message.short Added additional fixes to get 2.11 compiling. | |
| [info] git.commit.time 22.01.2015 @ 14:18:43 CST | |
| [info] git.remote.origin.url https://github.com/fnothaft/adam.git | |
| shouldExclude.apply(git.commit.user.email) = true | |
| shouldExclude.apply(git.commit.user.name) = true | |
| shouldExclude.apply(git.build.user.name) = true | |
| shouldExclude.apply(git.build.user.email) = true | |
| [info] git.build.time 22.01.2015 @ 14:36:58 CST | |
| [info] found property git.commit.id.abbrev | |
| [info] found property git.commit.message.full | |
| [info] found property git.commit.id | |
| [info] found property git.commit.message.short | |
| [info] found property git.commit.id.describe | |
| [info] found property git.branch | |
| [info] found property git.commit.time | |
| [info] found property git.build.time | |
| [info] found property git.remote.origin.url | |
| [info] Writing properties file to [ /Users/mheuer/working/fnothaft-adam/adam-core/src/main/resources/git.properties ] (for module ADAM: Core1 )... | |
| [info] ADAM ] project ADAM | |
| [info] ADAM: Core ] project ADAM: Core | |
| [info] ADAM: APIs for Java ] project ADAM: APIs for Java | |
| [info] ADAM: CLI ] project ADAM: CLI | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ adam-core_2.11 --- | |
| [INFO] Source directory: /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala added. | |
| [INFO] | |
| [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core_2.11 --- | |
| [INFO] Modified 0 of 254 .scala files | |
| [INFO] | |
| [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ adam-core_2.11 --- | |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. | |
| [INFO] Copying 2 resources | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:compile (scala-compile-first) @ adam-core_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.scala-lang.modules:scala-xml_2.11:1.0.1 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core_2.11:0.15.1-SNAPSHOT requires scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.2/scala-compiler-2.11.2.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.2/scala-compiler-2.11.2.jar (13261 KB at 9750.4 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.2/scala-compiler-2.11.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.2/scala-compiler-2.11.2.pom (3 KB at 79.6 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.jar (634 KB at 6961.3 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2.jar (407 KB at 5078.9 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.1/scala-library-2.11.1.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.1/scala-library-2.11.1.jar (5409 KB at 5297.1 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.1/scala-library-2.11.1.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-library/2.11.1/scala-library-2.11.1.pom (2 KB at 49.7 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2.pom | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.2/scala-parser-combinators_2.11-1.0.2.pom (3 KB at 67.9 KB/sec) | |
| [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile | |
| [INFO] Using incremental compilation | |
| [INFO] 'compiler-interface' not yet compiled for Scala 2.11.2. Compiling... | |
| [INFO] Compilation completed in 15.71 s | |
| [INFO] Compiling 168 Scala sources and 2 Java sources to /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/classes... | |
| [WARNING] /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala:29: no valid targets for annotation on value hdr - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) | |
| [WARNING] class SAMFileHeaderWritable(@transient hdr: SAMFileHeader) extends Serializable { | |
| [WARNING] ^ | |
| [WARNING] /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/parquet_reimpl/AvroParquetRDD.scala:54: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) | |
| [WARNING] class AvroIndexedParquetRDD[T <: IndexedRecord: ClassTag](@transient sc: SparkContext, | |
| [WARNING] ^ | |
| [WARNING] /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/parquet_reimpl/AvroParquetRDD.scala:109: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) | |
| [WARNING] class AvroParquetRDD[T <: IndexedRecord: ClassTag](@transient sc: SparkContext, | |
| [WARNING] ^ | |
| [WARNING] /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:121: abstract type pattern T is unchecked since it is eliminated by erasure | |
| [WARNING] case mappable: T => computePartition(extractReferenceRegion(mappable)) | |
| [WARNING] ^ | |
| [WARNING] /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/Coverage.scala:137: match may not be exhaustive. | |
| It would fail on the following input: (None, None) | |
| [WARNING] val points: RDD[OrientedPoint] = pairs.flatMap { | |
| [WARNING] ^ | |
| [WARNING] there were 5 deprecation warnings; re-run with -deprecation for details | |
| [WARNING] there were 39 feature warnings; re-run with -feature for details | |
| [WARNING] 7 warnings found | |
| [INFO] | |
| [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ adam-core_2.11 --- | |
| [INFO] Changes detected - recompiling the module! | |
| [INFO] Compiling 2 source files to /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/classes | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-test-source (add-test-source) @ adam-core_2.11 --- | |
| [INFO] Test Source directory: /Users/mheuer/working/fnothaft-adam/adam-core/src/test/scala added. | |
| [INFO] | |
| [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ adam-core_2.11 --- | |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. | |
| [INFO] Copying 55 resources | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:testCompile (scala-test-compile-first) @ adam-core_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.scala-lang.modules:scala-xml_2.11:1.0.1 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core_2.11:0.15.1-SNAPSHOT requires scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile | |
| [INFO] Using incremental compilation | |
| [INFO] Compiling 86 Scala sources to /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes... | |
| [WARNING] there was one feature warning; re-run with -feature for details | |
| [WARNING] one warning found | |
| [INFO] | |
| [INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ adam-core_2.11 --- | |
| [INFO] Nothing to compile - all classes are up to date | |
| [INFO] | |
| [INFO] --- maven-surefire-plugin:2.17:test (default-test) @ adam-core_2.11 --- | |
| [INFO] Tests are skipped. | |
| [INFO] | |
| [INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ adam-core_2.11 --- | |
| Discovery starting. | |
| Discovery completed in 1 second, 460 milliseconds. | |
| Run starting. Expected test count is: 426 | |
| TypePathSuite: | |
| - Two tail-less type pathes equal | |
| - Two identically tailed type pathes equal | |
| - Two type pathes equal with separately constructed tails | |
| +-------------------------+--------------------+--------+ | |
| | Col1 | Col2 | Col3 | | |
| +-------------------------+--------------------+--------+ | |
| | Col1Value1 | 100 nanoseconds | 100 | | |
| | Col1Value2 A Bit Longer | 200000 nanoseconds | 200000 | | |
| +-------------------------+--------------------+--------+ | |
| MonitorTableSuite: | |
| - Table is rendered correctly | |
| ZScoreNormalizationSuite: | |
| 2015-01-22 14:38:48 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable | |
| - compute mean of a set of samples | |
| - compute variance of a set of samples | |
| - variance should be 0 if all elements are the same | |
| - check z-score for a varying rdd | |
| RichGenotypeSuite: | |
| - different ploidy | |
| - all types for diploid genotype | |
| CredentialsPropertiesTestSuite: | |
| - Can parse a simple configuration file with CredentialsProperties | |
| GenotypeRDDFunctionsSuite: | |
| - concordance of identical and non-identical genotypes | |
| - concordance of identical VCFs should be 1.0 | |
| SparkMetricsSuite: | |
| - Task metrics are captured correctly | |
| - Stage metrics are captured correctly | |
| - Metrics are rendered correctly | |
| MdTagSuite: | |
| - null md tag | |
| - zero length md tag | |
| - md tag with non-digit initial value | |
| - md tag invalid base | |
| - md tag with no digit at end | |
| - md tag, pure insertion | |
| - md tag, pure insertion, test 2 | |
| - md tag pure insertion equality | |
| - md tag equality and hashcode | |
| - valid md tags | |
| - get start of read with no mismatches or deletions | |
| - get start of read with no mismatches, but with a deletion at the start | |
| - get start of read with mismatches at the start | |
| - get end of read with no mismatches or deletions | |
| - check that mdtag and rich record return same end | |
| - get end of read with no mismatches, but a deletion at end | |
| - get end of read with mismatches and a deletion at end | |
| - get correct string out of mdtag with no mismatches | |
| - get correct string out of mdtag with mismatches at start | |
| - get correct string out of mdtag with deletion at end | |
| - get correct string out of mdtag with mismatches at end | |
| - get correct string out of complex mdtag | |
| - check complex mdtag | |
| - move a cigar alignment by two for a read | |
| - rewrite alignment to all matches | |
| - rewrite alignment to two mismatches followed by all matches | |
| - rewrite alignment to include a deletion but otherwise all matches | |
| - rewrite alignment to include an insertion at the start of the read but otherwise all matches | |
| - create new md tag from read vs. reference, perfect match | |
| - create new md tag from read vs. reference, perfect alignment match, 1 mismatch | |
| - create new md tag from read vs. reference, alignment with deletion | |
| - create new md tag from read vs. reference, alignment with insert | |
| - handle '=' and 'X' operators | |
| ADAMRDDFunctionsSuite: | |
| - generate sequence dict from fasta | |
| - recover reference string from a single contig fragment | |
| - recover trimmed reference string from a single contig fragment | |
| - recover reference string from multiple contig fragments | |
| - recover trimmed reference string from multiple contig fragments | |
| GenotypePredicatesSuite: | |
| SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". | |
| SLF4J: Defaulting to no-operation (NOP) logger implementation | |
| SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. | |
| - Load only only PASSing records | |
| - Load all records and filter to only PASSing records | |
| Reads2PileupProcessorSuite: | |
| - can convert a single read with only matches | |
| - can convert a single read with matches and mismatches | |
| DNAPrefixTrieSuite: | |
| - it should not be possible to create an empty prefix trie | |
| - can retrieve all values with a completely-wildcard query | |
| - building a trie with illegal characters generates an IllegalArgumentException | |
| - kmers with ambiguous bases don't get added to the trie | |
| - building a trie fails if we have different length keys | |
| - insert keys into a trie, and retrieve them | |
| - perform a wildkey search | |
| - perform a prefix search | |
| - perform a suffix search | |
| - test getters | |
| GenotypesToVariantsConverterSuite: | |
| - Simple test of integer RMS | |
| - Simple test of floating point RMS | |
| - Max genotype quality should lead to max variant quality | |
| - Genotype quality = 0.5 for two samples should lead to variant quality of 0.75 | |
| PairingRDDSuite: | |
| - sliding on an empty RDD returns an empty RDD | |
| - sliding on an RDD where count() < width returns an empty RDD | |
| - sliding on an RDD where count() == width returns an RDD with one element. | |
| - sliding on a small RDD works correctly | |
| - sliding works correctly on a partitioned RDD | |
| - pairing a simple sequence works | |
| - pairing an empty sequence returns an empty sequence | |
| - pairing a sorted sequence works | |
| - pairWithEnds on an empty sequence returns an empty sequence | |
| - pairWithEnds gives us the right number and set of values | |
| GenotypesSummarySuite: | |
| - simple genotypes summary | |
| - empty genotypes summary | |
| ADAMVariationRDDFunctionsSuite: | |
| - recover samples from variant context | |
| - joins SNV database annotation | |
| ReferencePositionSuite: | |
| - create reference position from mapped read | |
| - create reference position from unmapped read | |
| - create reference position from mapped read but contig not specified | |
| - create reference position from mapped read but contig is underspecified | |
| - create reference position from mapped read but start not specified | |
| - create reference position from pileup | |
| - create reference position from variant | |
| - create reference position from genotype | |
| - liftOverToReference works with a multi-block alignment on the forward strand | |
| - liftOverToReference works with a multi-block alignment on the reverse strand | |
| - lift over between two transcripts on the forward strand | |
| - lift over between two transcripts on the reverse strand | |
| LengthNormalizationSuite: | |
| - normalize a single targeted region | |
| - normalize a set of targeted regions | |
| - calculate *pkm type normalization for a set of targeted regions | |
| DurationFormattingSuite: | |
| - Values with hours formatted correctly | |
| - Values with minutes formatted correctly | |
| - Values with seconds formatted correctly | |
| - Values with milliseconds formatted correctly | |
| - Values with microseconds formatted correctly | |
| - Values with nanoseconds formatted correctly | |
| ShuffleRegionJoinSuite: | |
| - Overlapping reference regions | |
| - Multiple reference regions do not throw exception | |
| - RegionJoin2 contains the same results as cartesianRegionJoin | |
| ConsensusGeneratorFromReadsSuite: | |
| - checking search for consensus list for artificial reads | |
| ConfigurationParserSuite: | |
| - parses a simple file | |
| ErrorCorrectionSuite: | |
| - cut a short read into qmers | |
| RowGroupRangeIndexSuite: | |
| - Can read simple test range index | |
| VCFLineParserSuite: | |
| - can parse a simple VCF | |
| - passing in the optional sampleSet parameter results in fewer columns being parsed | |
| - can convert into ADMAFlatGenotype records | |
| - passing in a sample subsets results in fewer FlatGenotype records being produced | |
| ComparisonTraversalEngineSuite: | |
| - generate works on a simple RDD | |
| - combine works on a simple RDD | |
| ADAMAlignmentRecordContextSuite: | |
| - loadADAMFromPaths can load simple RDDs that have just been saved | |
| - import records from interleaved FASTQ: 1 | |
| - import records from interleaved FASTQ: 2 | |
| - import records from interleaved FASTQ: 3 | |
| - import records from interleaved FASTQ: 4 | |
| - import records from single ended FASTQ: 1 | |
| - import records from single ended FASTQ: 2 | |
| - import records from single ended FASTQ: 3 | |
| - import records from single ended FASTQ: 4 | |
| - read properly paired fastq | |
| - read properly paired fastq and force pair fixing | |
| - read improperly paired fastq by noting size mismatch | |
| InterleavedFastqInputFormatSuite: | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.fq->interleaved_fastq_sample1.fq.output | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.fq->interleaved_fastq_sample2.fq.output | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.fq->interleaved_fastq_sample3.fq.output | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.fq->interleaved_fastq_sample4.fq.output | |
| ReferenceRegionSuite: | |
| - contains(: ReferenceRegion) | |
| - contains(: ReferencePosition) | |
| - merge | |
| - overlaps | |
| - distance(: ReferenceRegion) | |
| - distance(: ReferencePosition) | |
| - create region from unmapped read fails | |
| - create region from mapped read contains read start and end | |
| - validate that adjacent regions can be merged | |
| - validate that non-adjacent regions cannot be merged | |
| - compute convex hull of two sets | |
| - region name is sanitized when creating region from read | |
| - intersection fails on non-overlapping regions | |
| - compute intersection | |
| - build oriented reference region from non-oriented | |
| - comparison tests for oriented reference region | |
| - comparison tests for oriented reference region vs position | |
| - overlap tests for oriented reference region | |
| - check the width of a reference region | |
| AlignmentRecordReferenceMappingSuite: | |
| - test getReferenceId returns the right referenceId | |
| AlignmentRecordConverterSuite: | |
| - testing the fields in a converted ADAM Read | |
| - convert a read to fastq | |
| AvroParquetRDDSuite: | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| - Retrieve records from a Parquet file through classpath | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| - Using a projection works with classpath | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| Returning bytes from /Users/mheuer/working/fnothaft-adam/adam-core/target/scala-2.11.2/test-classes/reads-0-2-0 | |
| - Using a filter works with classpath | |
| IntervalListReaderSuite: | |
| - Can read the simple GATK-supplied example interval list file | |
| SingleFastqInputFormatSuite: | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample1.fq->single_fastq_sample1.fq.output | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample2.fq->single_fastq_sample2.fq.output | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample3.fq->single_fastq_sample3.fq.output | |
| - interleaved FASTQ hadoop reader: interleaved_fastq_sample4.fq->single_fastq_sample4.fq.output | |
| TrimReadsSuite: | |
| - trim a few md tags | |
| - trim a few cigars that just have clipping and matches | |
| - trim cigars with indels | |
| - trim a few reads | |
| - correctly trim an RDD of reads | |
| - adaptively trim reads | |
| FeatureParsingSuite: | |
| - Can read a .gtf file | |
| - Can read a .bed file | |
| - Can read a .narrowPeak file | |
| RegExpSuite: | |
| - matches returns Some(matcher) when a complete match is found | |
| - find returns Some(matcher) when a partial match is found | |
| AttributeUtilsSuite: | |
| - parseTags returns a reasonable set of tagStrings | |
| - empty string is parsed as zero tagStrings | |
| - incorrectly formatted tag throws an exception | |
| - string tag with a ':' in it is correctly parsed | |
| MarkDuplicatesSuite: | |
| - single read | |
| - reads at different positions | |
| - reads at the same position | |
| - reads at the same position with clipping | |
| - reads on reverse strand | |
| - unmapped reads | |
| - read pairs | |
| - read pairs with fragments | |
| - quality scores | |
| - read pairs that cross chromosomes | |
| ServoTimerSuite: | |
| - Total time computed correctly | |
| - Count computed correctly | |
| - Mean computed correctly | |
| - Max computed correctly | |
| - Min computed correctly | |
| - Timer and sub-monitors tagged correctly | |
| - Nanosecond timings recorded correctly | |
| ParquetCommonSuite: | |
| - Can load footer from small vcf | |
| IndelRealignmentTargetSuite: | |
| - checking simple realignment target | |
| - creating simple target from read with deletion | |
| - creating simple target from read with insertion | |
| - joining simple realignment targets on same chr | |
| - joining simple realignment targets on different chr throws exception | |
| - creating targets from three intersecting reads, same indel | |
| - creating targets from three intersecting reads, two different indel | |
| - creating targets from two disjoint reads | |
| - creating targets for artificial reads: one-by-one | |
| - creating targets for artificial reads: all-at-once (merged) | |
| - creating indel targets for mason reads | |
| TwoBitSuite: | |
| - correctly read sequence from .2bit file | |
| RecordConditionSuite: | |
| - create record condition from simple field condition | |
| - create record condition from nested field condition | |
| - create record condition from multiple field conditions | |
| - create record condition from non-equality field conditions | |
| - create record condition OR of record conditions | |
| - high quality adam read condition | |
| - passing genotype record condition | |
| GeneratorFilterSuite: | |
| - CombinedFilter combines two independent filters | |
| ASCIITableSuite: | |
| - Table is rendered correctly | |
| - Inequal sizes between header and rows are rejected | |
| ConsensusSuite: | |
| - test the insertion of a consensus insertion into a reference | |
| - test the insertion of a consensus deletion into a reference | |
| - inserting empty consensus returns the reference | |
| DecadentReadSuite: | |
| - reference position of decadent read | |
| - reference position of decadent read with insertions | |
| FieldEnumerationSuite: | |
| - Empty projections are illegal | |
| - Simple projection on Read works | |
| BroadcastRegionJoinSuite: | |
| - alternating returns an alternating seq of items | |
| - Single region returns itself | |
| - Two adjacent regions will be merged | |
| - Nonoverlapping regions will all be returned | |
| - Many overlapping regions will all be merged | |
| - ADAMRecords return proper references | |
| - Ensure same reference regions get passed together | |
| - Overlapping reference regions | |
| - Multiple reference regions do not throw exception | |
| - regionJoin contains the same results as cartesianRegionJoin | |
| CoverageSuite: | |
| - regionToWindows | |
| - calculate empty coverage | |
| - calculate coverage of one region | |
| - calculate coverage of two regions | |
| - calculate coverage of three regions | |
| - calculate coverage of two adjacent regions | |
| - calculate coverage of two nearby regions | |
| - calculate coverage of three out-of-order regions | |
| - calculate coverage of two regions which join at a window boundary | |
| - find empty coverage | |
| - find coverage of one region | |
| - find coverage of two regions | |
| - find coverage of three regions | |
| - find coverage of two adjacent regions | |
| - find coverage of two nearby regions | |
| - find coverage of three out-of-order regions | |
| - find coverage of two regions which join at a window boundary | |
| VariantContextConverterSuite: | |
| - Convert GATK site-only SNV to ADAM | |
| - Convert GATK site-only SNV to ADAM with contig conversion | |
| - Convert GATK site-only CNV to ADAM | |
| - Convert GATK SNV w/ genotypes w/ phase information to ADAM | |
| - Convert GATK SNV with different filters to ADAM | |
| - Convert ADAM site-only SNV to GATK | |
| - Convert ADAM site-only SNV to GATK with contig conversion | |
| - Convert ADAM SNV w/ genotypes to GATK | |
| - Convert GATK multi-allelic sites-only SNVs to ADAM | |
| - Convert GATK multi-allelic SNVs to ADAM | |
| - Convert gVCF reference records to ADAM | |
| AttributeSuite: | |
| - test SAMTagAndValue parsing | |
| RangeIndexGeneratorSuite: | |
| - small_adam_A.fgenotype is indexed into one RangeIndexEntry | |
| LocalFileLocatorSuite: | |
| - parentLocator retrieves the parent directory | |
| - relativeLocator retrieves a subdirectory | |
| - bytes accesses the named underlying file | |
| ADAMContextSuite: | |
| - sc.adamLoad should not fail on unmapped reads | |
| - sc.adamLoad should not load a file without a type specified | |
| - can read a small .SAM file | |
| - can filter a .SAM file based on quality | |
| - Can convert to phred | |
| - Can convert from phred | |
| - findFiles correctly finds a nested set of directories | |
| ADAMVariationContextSuite: | |
| - can read a small .vcf file | |
| 2015-01-22 14:41:18 WARN VariationContext:81 - Setting header for partition 0 | |
| 2015-01-22 14:41:18 WARN VariationContext:81 - Setting header for partition 1 | |
| 2015-01-22 14:41:18 WARN VariationContext:81 - Setting header for partition 2 | |
| 2015-01-22 14:41:18 WARN VariationContext:87 - Set VCF header for partition 2 | |
| 2015-01-22 14:41:18 WARN VariationContext:87 - Set VCF header for partition 1 | |
| 2015-01-22 14:41:18 WARN VariationContext:87 - Set VCF header for partition 0 | |
| 2015-01-22 14:41:18 WARN VariationContext:81 - Setting header for partition 3 | |
| 2015-01-22 14:41:18 WARN VariationContext:87 - Set VCF header for partition 3 | |
| - can write, then read in .vcf file | |
| RDDFunSuite: | |
| ByteAccessSuite: | |
| - ByteArrayByteAccess returns arbitrary subsets of bytes correctly | |
| - ByteArrayByteAccess supports two successive calls with different offsets | |
| - LocalFileByteAccess returns arbitrary subsets of bytes correctly | |
| ParquetListerSuite: | |
| - can list a single small parquet file | |
| - can list all the records in a directory | |
| - directories with no parquet files should have 0 records | |
| - uses projections properly | |
| AggregatorSuite: | |
| - UniqueAggregator only collects unique values | |
| - HistogramAggregator counts values correctly | |
| FileLocatorSuite: | |
| - parseSlash can correctly parse a one-slash string | |
| - parseSlash can correctly parse a two-slash string | |
| - parseSlash can correctly parse a no-slash string | |
| RichCigarSuite: | |
| - moving 2 bp from a deletion to a match operator | |
| - moving 2 bp from a insertion to a match operator | |
| - moving 1 base in a two element cigar | |
| - move to start of read | |
| UtilSuite: | |
| - isSameConfig | |
| ComparisonsSuite: | |
| - Dupe mismatches found | |
| - Mismatched mapped positions histogram generated | |
| - Test map quality scores | |
| - Test base quality scores | |
| FeatureHierarchySuite: | |
| - Feature values converted into GTFFeatures retain their aligned positions in the fields of ReferenceRegion | |
| NormalizationUtilsSuite: | |
| - cannot move an indel left if there are no bases to it's left | |
| - move a simple indel to farthest position left until bases run out | |
| - move a simple indel to farthest position left, past length of indel | |
| - cannot move a left normalized indel in a short tandem repeat | |
| - move an indel in a short tandem repeat | |
| - move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length | |
| - moving a simple read with single deletion that cannot shift | |
| - shift an indel left by 0 in a cigar | |
| - shift an indel left by 1 in a cigar | |
| - do not left align a complex read which is already left aligned | |
| SmithWatermanSuite: | |
| - gather max position from simple scoring matrix | |
| - gather max position from irregular scoring matrix | |
| - gather max position from irregular scoring matrix with deletions | |
| - score simple alignment with constant gap | |
| - score irregular scoring matrix | |
| - score irregular scoring matrix with indel | |
| - can unroll cigars correctly | |
| - execute simple trackback | |
| - execute trackback with indel | |
| - run end to end smith waterman for simple reads | |
| - run end to end smith waterman for short sequences with indel | |
| - run end to end smith waterman for longer sequences with snp | |
| - run end to end smith waterman for longer sequences with short indel | |
| - run end to end smith waterman for shorter sequence in longer sequence | |
| - run end to end smith waterman for shorter sequence in longer sequence, with indel | |
| FastaConverterSuite: | |
| - find contig index | |
| - convert a single record without naming information | |
| - convert a single record with naming information | |
| - convert single fasta sequence | |
| - convert fasta with multiple sequences | |
| - convert fasta with multiple sequences; short fragment | |
| - convert reference fasta file | |
| IndelTableSuite: | |
| - check for indels in a region with known indels | |
| - check for indels in a contig that doesn't exist | |
| - check for indels in a region without known indels | |
| - build indel table from rdd of variants | |
| 2015-01-22 14:41:39 WARN ConfigurationParser:71 - File "/foo/bar.conf" does not exist, using default values. | |
| ConfigurationFileSuite: | |
| - Can read values out of a file | |
| - Reads default values when the file does not exist. | |
| - Does not read the default values, when the file does exist. | |
| RealignIndelsSuite: | |
| - checking mapping to targets for artificial reads | |
| - checking alternative consensus for artificial reads | |
| - checking extraction of reference from reads | |
| - checking realigned reads for artificial input | |
| - test mismatch quality scoring | |
| - test mismatch quality scoring for no mismatches | |
| - test mismatch quality scoring after unpacking read | |
| - we shouldn't try to realign a region with no target | |
| - we shouldn't try to realign reads with no indel evidence | |
| - test OP and OC tags | |
| BaseQualityRecalibrationSuite: | |
| - BQSR Test Input #1 | |
| - BQSR Test Input #1 w/ VCF Sites | |
| ADAMAlignmentRecordRDDFunctionsSuite: | |
| - sorting reads | |
| - convert an RDD of reads into rods | |
| - convert an RDD of reads into rods, different references | |
| - characterizeTags counts integer tag values correctly | |
| - withTag returns only those records which have the appropriate tag | |
| - withTag, when given a tag name that doesn't exist in the input, returns an empty RDD | |
| - characterizeTagValues counts distinct values of a tag | |
| - characterizeTags counts tags in a SAM file correctly | |
| - round trip from ADAM to SAM and back to ADAM produces equivalent Read values | |
| - SAM conversion sets read mapped flag properly | |
| - round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values | |
| - round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values | |
| AvroIndexedParquetRDDSuite: | |
| - S3AvroIndexedParquetRDD can read a local index and produce the correct records | |
| - S3AvroIndexedParquetRDD produces no partitions, if the query overlaps no read groups | |
| - produces 1 partition when the filter only overlaps one partition !!! IGNORED !!! | |
| - indexing produces the same records as the non-indexed RDD !!! IGNORED !!! | |
| ProgramRecordSuite: | |
| - convert a sam program record with no optional fields into a program record and v/v | |
| - convert a sam program record into a program record and v/v | |
| SequenceDictionarySuite: | |
| - Convert from sam sequence record and back | |
| - Convert from SAM sequence dictionary file (with extra fields) | |
| - merge into existing dictionary | |
| - Convert from SAM sequence dictionary and back | |
| - Can retrieve sequence by name | |
| - SequenceDictionary's with same single element are equal | |
| - SequenceDictionary's with same two elements are equals | |
| - SequenceDictionary's with different elements are unequal | |
| - SequenceDictionaries with same elements in different order are compatible | |
| - isCompatible tests equality on overlap | |
| - The addition + works correctly | |
| - The append operation ++ works correctly | |
| - ContainsRefName works correctly for different string types | |
| - Apply on name works correctly for different String types | |
| - convert from sam sequence record and back | |
| - convert from sam sequence dictionary and back | |
| HistogramSuite: | |
| - Histogram addition works | |
| GenomicPositionPartitionerSuite: | |
| - partitions the UNMAPPED ReferencePosition into the top partition | |
| - partitioning into N pieces on M total sequence length, where N > M, results in M partitions | |
| - correctly partitions a single dummy sequence into two pieces | |
| - correctly counts cumulative lengths | |
| - correctly partitions positions across two dummy sequences | |
| 2015-01-22 14:42:24 WARN TaskSetManager:71 - Stage 0 contains a task of very large size (105 KB). The maximum recommended task size is 100 KB. | |
| 2015-01-22 14:42:24 WARN TaskSetManager:71 - Stage 1 contains a task of very large size (105 KB). The maximum recommended task size is 100 KB. | |
| - test that we can range partition ADAMRecords | |
| 2015-01-22 14:42:25 WARN ADAMContext:242 - Projection is ignored when loading a BAM file | |
| - test that simple partitioning works okay on a reasonable set of ADAMRecords | |
| RichAlignmentRecordSuite: | |
| - referenceLengthFromCigar | |
| - Unclipped Start | |
| - Unclipped End | |
| - Illumina Optics | |
| - Cigar Clipping Sequence | |
| - tags contains optional fields | |
| - Reference Positions | |
| - read overlap unmapped read | |
| - read overlap reference position | |
| - read overlap same position different contig | |
| ByteArrayLocatorSuite: | |
| - byte access can be wrapped in a locator correctly | |
| ADAMPileupRDDFunctionsSuite: | |
| - can convert pileups to rods, bases at different pos, same reference | |
| - can convert pileups to rods, bases at same pos, different reference | |
| - can convert pileups to rods, bases at same pos | |
| - can convert pileups to rods, bases at same pos, split by different sample | |
| - can convert pileups to rods, bases at same pos, split by same sample | |
| - check coverage, bases at different pos | |
| - check coverage, bases at same pos | |
| GeneSuite: | |
| - can load a set of gene models from an Ensembl GTF file | |
| - can load a set of gene models from a Gencode GTF file | |
| - chr20 gencode transcript sequences match the published sequences | |
| ADAMMetricsListenerSuite: | |
| - Listener accumulates metrics when registered with Spark | |
| TrackedLayoutSuite: | |
| - OrderedTrackedLayout lays out no records into zero tracks | |
| - OrderedTrackedLayout lays out AlignmentRecords left-to-right in the order they're passed | |
| - OrderedTrackedLayout can handle unaligned reads | |
| MapToolsSuite: | |
| - add two nonzero integer maps | |
| - add two nonzero float maps | |
| - adding an empty map is the identity | |
| RecordGroupDictionarySuite: | |
| - simple conversion to and from sam read group | |
| - sample name must be set | |
| - create a record group from a read | |
| - don't create a record group from a read without record group info | |
| - simple equality checks | |
| Run completed in 3 minutes, 55 seconds. | |
| Total number of tests run: 426 | |
| Suites: completed 88, aborted 0 | |
| Tests: succeeded 426, failed 0, canceled 0, ignored 2, pending 0 | |
| All tests passed. | |
| [INFO] | |
| [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ adam-core_2.11 --- | |
| [INFO] Building jar: /Users/mheuer/working/fnothaft-adam/adam-core/target/adam-core_2.11-0.15.1-SNAPSHOT.jar | |
| [INFO] | |
| [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ adam-core_2.11 --- | |
| [INFO] Building jar: /Users/mheuer/working/fnothaft-adam/adam-core/target/adam-core_2.11-0.15.1-SNAPSHOT-tests.jar | |
| [INFO] | |
| [INFO] >>> scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) > generate-sources @ adam-core_2.11 >>> | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core_2.11 --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core_2.11 --- | |
| [INFO] | |
| [INFO] --- git-commit-id-plugin:2.1.9:revision (default) @ adam-core_2.11 --- | |
| [info] dotGitDirectory /Users/mheuer/working/fnothaft-adam/.git | |
| [info] git.build.user.name Michael Heuer | |
| [info] git.build.user.email heuermh@acm.org | |
| [info] git.branch split-compile | |
| [info] Tag refs [ [Ref[refs/tags/adam-parent-0.6.0=cc1d98f4cb95b63f7f4b2ab4768843cce51a3a9c]] ] | |
| [info] Resolved tag [ adam-parent-0.6.0 ] [ PersonIdent[Matt Massie, massie@cs.berkeley.edu, Sun Jan 19 12:43:54 2014 -0800] ], points at [ commit 5fe4f1cdca401bdfb036c3ce4132259abc56d019 0 ------ ] | |
| [info] key [ commit 5fe4f1cdca401bdfb036c3ce4132259abc56d019 0 ------ ], tags => [ [DatedRevTag{id=cc1d98f4cb95b63f7f4b2ab4768843cce51a3a9c, tagName='adam-parent-0.6.0', date=January 19, 2014 2:43:54 PM CST}] ] | |
| [info] Created map: [ {commit 5fe4f1cdca401bdfb036c3ce4132259abc56d019 0 ------=[adam-parent-0.6.0]} ] | |
| [info] HEAD is [ 5cc2b324c9d8860a8698296191236846996e1915 ] | |
| [info] Repo is in dirty state [ true ] | |
| [info] git.commit.id.describe adam-parent-0.6.0-721-g5cc2b32 | |
| [info] git.commit.id 5cc2b324c9d8860a8698296191236846996e1915 | |
| [info] git.commit.id.abbrev 5cc2b32 | |
| [info] git.commit.user.name Frank Austin Nothaft | |
| [info] git.commit.user.email fnothaft@alumni.stanford.edu | |
| [info] git.commit.message.full Added additional fixes to get 2.11 compiling. | |
| [info] git.commit.message.short Added additional fixes to get 2.11 compiling. | |
| [info] git.commit.time 22.01.2015 @ 14:18:43 CST | |
| [info] git.remote.origin.url https://github.com/fnothaft/adam.git | |
| shouldExclude.apply(git.commit.user.email) = true | |
| shouldExclude.apply(git.commit.user.name) = true | |
| shouldExclude.apply(git.build.user.name) = true | |
| shouldExclude.apply(git.build.user.email) = true | |
| [info] git.build.time 22.01.2015 @ 14:42:44 CST | |
| [info] found property git.commit.id.abbrev | |
| [info] found property git.commit.message.full | |
| [info] found property git.commit.id | |
| [info] found property git.commit.message.short | |
| [info] found property git.commit.id.describe | |
| [info] found property git.branch | |
| [info] found property git.commit.time | |
| [info] found property git.build.time | |
| [info] found property git.remote.origin.url | |
| [info] Writing properties file to [ /Users/mheuer/working/fnothaft-adam/adam-core/src/main/resources/git.properties ] (for module ADAM: Core2 )... | |
| [info] ADAM ] project ADAM | |
| [info] ADAM: Core ] project ADAM: Core | |
| [info] ADAM: APIs for Java ] project ADAM: APIs for Java | |
| [info] ADAM: CLI ] project ADAM: CLI | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ adam-core_2.11 --- | |
| [INFO] Source directory: /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala added. | |
| [INFO] | |
| [INFO] <<< scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) < generate-sources @ adam-core_2.11 <<< | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) @ adam-core_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.scala-lang.modules:scala-xml_2.11:1.0.1 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core_2.11:0.15.1-SNAPSHOT requires scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.scala-lang.modules:scala-xml_2.11:1.0.1 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core_2.11:0.15.1-SNAPSHOT requires scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:146: warning: discarding unmoored doc comment | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala:359: warning: discarding unmoored doc comment | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala:384: warning: discarding unmoored doc comment | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:59: warning: discarding unmoored doc comment | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala:29: warning: no valid targets for annotation on value hdr - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) | |
| class SAMFileHeaderWritable(@transient hdr: SAMFileHeader) extends Serializable { | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/parquet_reimpl/AvroParquetRDD.scala:54: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) | |
| class AvroIndexedParquetRDD[T <: IndexedRecord: ClassTag](@transient sc: SparkContext, | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/parquet_reimpl/AvroParquetRDD.scala:109: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) | |
| class AvroParquetRDD[T <: IndexedRecord: ClassTag](@transient sc: SparkContext, | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:121: warning: abstract type pattern T is unchecked since it is eliminated by erasure | |
| case mappable: T => computePartition(extractReferenceRegion(mappable)) | |
| ^ | |
| warning: there were 39 feature warnings; re-run with -feature for details | |
| model contains 438 documentable templates | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/normalization/ZScoreNormalization.scala:26: warning: Tag '@returns' is not recognised | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/MonitorTable.scala:26: warning: Could not find any member to link for "Monitor". | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/MonitorTable.scala:26: warning: Could not find any member to link for "String". | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/ServoTimer.scala:30: warning: Could not find any member to link for "com.netflix.servo.monitor.CompositeMonitor". | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/MonitorTable.scala:76: warning: Could not find any member to link for "Monitor". | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/MonitorTable.scala:76: warning: Could not find any member to link for "CompositeMonitor". | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/instrumentation/ASCIITable.scala:39: warning: Could not find any member to link for "PrintStream". | |
| /** | |
| ^ | |
| /Users/mheuer/working/fnothaft-adam/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala:28: warning: Tag '@readName' is not recognised | |
| /** | |
| ^ | |
| 17 warnings found | |
| [INFO] Building jar: /Users/mheuer/working/fnothaft-adam/adam-core/target/adam-core_2.11-0.15.1-SNAPSHOT-javadoc.jar | |
| [INFO] | |
| [INFO] --- maven-install-plugin:2.5.1:install (default-install) @ adam-core_2.11 --- | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-core/target/adam-core_2.11-0.15.1-SNAPSHOT.jar to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-core_2.11/0.15.1-SNAPSHOT/adam-core_2.11-0.15.1-SNAPSHOT.jar | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-core/pom.xml to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-core_2.11/0.15.1-SNAPSHOT/adam-core_2.11-0.15.1-SNAPSHOT.pom | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-core/target/adam-core_2.11-0.15.1-SNAPSHOT-tests.jar to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-core_2.11/0.15.1-SNAPSHOT/adam-core_2.11-0.15.1-SNAPSHOT-tests.jar | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-core/target/adam-core_2.11-0.15.1-SNAPSHOT-javadoc.jar to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-core_2.11/0.15.1-SNAPSHOT/adam-core_2.11-0.15.1-SNAPSHOT-javadoc.jar | |
| [INFO] | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Building ADAM: APIs for Java 0.15.1-SNAPSHOT | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] | |
| [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ adam-apis_2.11 --- | |
| [INFO] Deleting /Users/mheuer/working/fnothaft-adam/adam-apis/target | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis_2.11 --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis_2.11 --- | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ adam-apis_2.11 --- | |
| [INFO] Source directory: /Users/mheuer/working/fnothaft-adam/adam-apis/src/main/scala added. | |
| [INFO] | |
| [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis_2.11 --- | |
| [INFO] Modified 0 of 4 .scala files | |
| [INFO] | |
| [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ adam-apis_2.11 --- | |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. | |
| [INFO] skip non existing resourceDirectory /Users/mheuer/working/fnothaft-adam/adam-apis/src/main/resources | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:compile (scala-compile-first) @ adam-apis_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile | |
| [INFO] Using incremental compilation | |
| [INFO] Compiling 3 Scala sources to /Users/mheuer/working/fnothaft-adam/adam-apis/target/scala-2.11.2/classes... | |
| [WARNING] there were two feature warnings; re-run with -feature for details | |
| [WARNING] one warning found | |
| [INFO] | |
| [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ adam-apis_2.11 --- | |
| [INFO] Nothing to compile - all classes are up to date | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-test-source (add-test-source) @ adam-apis_2.11 --- | |
| [INFO] Test Source directory: /Users/mheuer/working/fnothaft-adam/adam-apis/src/test/scala added. | |
| [INFO] | |
| [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ adam-apis_2.11 --- | |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. | |
| [INFO] Copying 1 resource | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:testCompile (scala-test-compile-first) @ adam-apis_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile | |
| [INFO] Using incremental compilation | |
| [INFO] Compiling 1 Scala source and 2 Java sources to /Users/mheuer/working/fnothaft-adam/adam-apis/target/scala-2.11.2/test-classes... | |
| [INFO] | |
| [INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ adam-apis_2.11 --- | |
| [INFO] Changes detected - recompiling the module! | |
| [INFO] Compiling 2 source files to /Users/mheuer/working/fnothaft-adam/adam-apis/target/scala-2.11.2/test-classes | |
| [INFO] | |
| [INFO] --- maven-surefire-plugin:2.17:test (default-test) @ adam-apis_2.11 --- | |
| [INFO] Tests are skipped. | |
| [INFO] | |
| [INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ adam-apis_2.11 --- | |
| Discovery starting. | |
| Discovery completed in 157 milliseconds. | |
| Run starting. Expected test count is: 2 | |
| JavaADAMContextSuite: | |
| 2015-01-22 14:43:29 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable | |
| - can read a small .SAM file | |
| SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". | |
| SLF4J: Defaulting to no-operation (NOP) logger implementation | |
| SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. | |
| - can read a small .SAM file inside of java | |
| Run completed in 6 seconds, 646 milliseconds. | |
| Total number of tests run: 2 | |
| Suites: completed 2, aborted 0 | |
| Tests: succeeded 2, failed 0, canceled 0, ignored 0, pending 0 | |
| All tests passed. | |
| [INFO] | |
| [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ adam-apis_2.11 --- | |
| [INFO] Building jar: /Users/mheuer/working/fnothaft-adam/adam-apis/target/adam-apis_2.11-0.15.1-SNAPSHOT.jar | |
| [INFO] | |
| [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ adam-apis_2.11 --- | |
| [INFO] Building jar: /Users/mheuer/working/fnothaft-adam/adam-apis/target/adam-apis_2.11-0.15.1-SNAPSHOT-tests.jar | |
| [INFO] | |
| [INFO] >>> scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) > generate-sources @ adam-apis_2.11 >>> | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis_2.11 --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis_2.11 --- | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ adam-apis_2.11 --- | |
| [INFO] Source directory: /Users/mheuer/working/fnothaft-adam/adam-apis/src/main/scala added. | |
| [INFO] | |
| [INFO] <<< scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) < generate-sources @ adam-apis_2.11 <<< | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:doc-jar (attach-scaladocs) @ adam-apis_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-ast_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-core_2.11:3.2.10 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| warning: there were two feature warnings; re-run with -feature for details | |
| model contains 11 documentable templates | |
| one warning found | |
| [INFO] Building jar: /Users/mheuer/working/fnothaft-adam/adam-apis/target/adam-apis_2.11-0.15.1-SNAPSHOT-javadoc.jar | |
| [INFO] | |
| [INFO] --- maven-install-plugin:2.5.1:install (default-install) @ adam-apis_2.11 --- | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-apis/target/adam-apis_2.11-0.15.1-SNAPSHOT.jar to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-apis_2.11/0.15.1-SNAPSHOT/adam-apis_2.11-0.15.1-SNAPSHOT.jar | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-apis/pom.xml to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-apis_2.11/0.15.1-SNAPSHOT/adam-apis_2.11-0.15.1-SNAPSHOT.pom | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-apis/target/adam-apis_2.11-0.15.1-SNAPSHOT-tests.jar to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-apis_2.11/0.15.1-SNAPSHOT/adam-apis_2.11-0.15.1-SNAPSHOT-tests.jar | |
| [INFO] Installing /Users/mheuer/working/fnothaft-adam/adam-apis/target/adam-apis_2.11-0.15.1-SNAPSHOT-javadoc.jar to /Users/mheuer/.m2/repository/org/bdgenomics/adam/adam-apis_2.11/0.15.1-SNAPSHOT/adam-apis_2.11-0.15.1-SNAPSHOT-javadoc.jar | |
| [INFO] | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Building ADAM: CLI 0.15.1-SNAPSHOT | |
| [INFO] ------------------------------------------------------------------------ | |
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| Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/scalate/scalate-util_2.11/1.7.0/scalate-util_2.11-1.7.0.jar (297 KB at 1483.8 KB/sec) | |
| Downloading: https://repo.maven.apache.org/maven2/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar | |
| Downloaded: https://repo.maven.apache.org/maven2/org/clapper/grizzled-slf4j_2.11/1.0.2/grizzled-slf4j_2.11-1.0.2.jar (7 KB at 26.0 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/scalatra-json_2.11/2.3.0/scalatra-json_2.11-2.3.0.jar (83 KB at 327.7 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar (221 KB at 550.8 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/scalatra_2.11/2.3.0/scalatra_2.11-2.3.0.jar (1166 KB at 2317.8 KB/sec) | |
| Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/scalate/scalate-core_2.11/1.7.0/scalate-core_2.11-1.7.0.jar (1920 KB at 1398.0 KB/sec) | |
| [INFO] | |
| [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ adam-cli_2.11 --- | |
| [INFO] Deleting /Users/mheuer/working/fnothaft-adam/adam-cli/target | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli_2.11 --- | |
| [INFO] | |
| [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli_2.11 --- | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ adam-cli_2.11 --- | |
| [INFO] Source directory: /Users/mheuer/working/fnothaft-adam/adam-cli/src/main/scala added. | |
| [INFO] | |
| [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli_2.11 --- | |
| [INFO] Modified 0 of 39 .scala files | |
| [INFO] | |
| [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ adam-cli_2.11 --- | |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. | |
| [INFO] Copying 1 resource | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:compile (scala-compile-first) @ adam-cli_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.scala-lang.modules:scala-xml_2.11:1.0.1 requires scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core:0.15.1-20150122.151900-314 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core:0.15.1-20150122.151900-314 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-apis:0.15.1-20150122.151932-312 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-apis:0.15.1-20150122.151932-312 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-cli_2.11:0.15.1-SNAPSHOT requires scala version: 2.11.2 | |
| [WARNING] org.scalatra.scalate:scalate-util_2.11:1.7.0 requires scala version: 2.11.2 | |
| [WARNING] org.scalatra.scalate:scalate-core_2.11:1.7.0 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile | |
| [INFO] Using incremental compilation | |
| [INFO] Compiling 36 Scala sources to /Users/mheuer/working/fnothaft-adam/adam-cli/target/scala-2.11.2/classes... | |
| [WARNING] there was one deprecation warning; re-run with -deprecation for details | |
| [WARNING] one warning found | |
| [INFO] | |
| [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ adam-cli_2.11 --- | |
| [INFO] Nothing to compile - all classes are up to date | |
| [INFO] | |
| [INFO] --- build-helper-maven-plugin:1.7:add-test-source (add-test-source) @ adam-cli_2.11 --- | |
| [INFO] Test Source directory: /Users/mheuer/working/fnothaft-adam/adam-cli/src/test/scala added. | |
| [INFO] | |
| [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ adam-cli_2.11 --- | |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. | |
| [INFO] Copying 3 resources | |
| [INFO] | |
| [INFO] --- scala-maven-plugin:3.2.0:testCompile (scala-test-compile-first) @ adam-cli_2.11 --- | |
| [WARNING] Expected all dependencies to require Scala version: 2.11.2 | |
| [WARNING] com.twitter:chill_2.11:0.5.0 requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-remote_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-actor_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.spark-project.akka:akka-slf4j_2.11:2.3.4-spark requires scala version: 2.11.2 | |
| [WARNING] org.apache.spark:spark-core_2.11:1.2.0 requires scala version: 2.11.2 | |
| [WARNING] org.json4s:json4s-jackson_2.11:3.2.10 requires scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.scala-lang.modules:scala-xml_2.11:1.0.1 requires scala version: 2.11.2 | |
| [WARNING] org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core:0.15.1-20150122.151900-314 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-core:0.15.1-20150122.151900-314 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-apis:0.15.1-20150122.151932-312 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-apis:0.15.1-20150122.151932-312 requires scala version: 2.11.2 | |
| [WARNING] org.bdgenomics.adam:adam-cli_2.11:0.15.1-SNAPSHOT requires scala version: 2.11.2 | |
| [WARNING] org.scalatra.scalate:scalate-util_2.11:1.7.0 requires scala version: 2.11.2 | |
| [WARNING] org.scalatra.scalate:scalate-core_2.11:1.7.0 requires scala version: 2.11.0 | |
| [WARNING] Multiple versions of scala libraries detected! | |
| [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile | |
| [INFO] Using incremental compilation | |
| [INFO] Compiling 3 Scala sources to /Users/mheuer/working/fnothaft-adam/adam-cli/target/scala-2.11.2/test-classes... | |
| [INFO] | |
| [INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ adam-cli_2.11 --- | |
| [INFO] Nothing to compile - all classes are up to date | |
| [INFO] | |
| [INFO] --- maven-surefire-plugin:2.17:test (default-test) @ adam-cli_2.11 --- | |
| [INFO] Tests are skipped. | |
| [INFO] | |
| [INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ adam-cli_2.11 --- | |
| Discovery starting. | |
| Discovery completed in 293 milliseconds. | |
| Run starting. Expected test count is: 14 | |
| Features2ADAMSuite: | |
| - can convert a simple BED file !!! IGNORED !!! | |
| 2015-01-22 14:44:58 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable | |
| SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". | |
| SLF4J: Defaulting to no-operation (NOP) logger implementation | |
| SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. | |
| *** RUN ABORTED *** | |
| java.lang.NoClassDefFoundError: scala/collection/GenTraversableOnce$class | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetPartition$$anon$1.<init>(ParquetPartition.scala:125) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetPartition$.materializeRecords(ParquetPartition.scala:125) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetLister.org$bdgenomics$adam$parquet_reimpl$ParquetLister$$materialize(ParquetLister.scala:80) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetLister$$anonfun$materialize$5.apply(ParquetLister.scala:148) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetLister$$anonfun$materialize$5.apply(ParquetLister.scala:145) | |
| at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:252) | |
| at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:252) | |
| at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) | |
| at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) | |
| at scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:252) | |
| ... | |
| Cause: java.lang.ClassNotFoundException: scala.collection.GenTraversableOnce$class | |
| at java.net.URLClassLoader$1.run(URLClassLoader.java:366) | |
| at java.net.URLClassLoader$1.run(URLClassLoader.java:355) | |
| at java.security.AccessController.doPrivileged(Native Method) | |
| at java.net.URLClassLoader.findClass(URLClassLoader.java:354) | |
| at java.lang.ClassLoader.loadClass(ClassLoader.java:425) | |
| at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) | |
| at java.lang.ClassLoader.loadClass(ClassLoader.java:358) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetPartition$$anon$1.<init>(ParquetPartition.scala:125) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetPartition$.materializeRecords(ParquetPartition.scala:125) | |
| at org.bdgenomics.adam.parquet_reimpl.ParquetLister.org$bdgenomics$adam$parquet_reimpl$ParquetLister$$materialize(ParquetLister.scala:80) | |
| ... | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Reactor Summary: | |
| [INFO] | |
| [INFO] ADAM ............................................... SUCCESS [ 7.698 s] | |
| [INFO] ADAM: Core ......................................... SUCCESS [06:25 min] | |
| [INFO] ADAM: APIs for Java ................................ SUCCESS [ 25.673 s] | |
| [INFO] ADAM: CLI .......................................... FAILURE [01:20 min] | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] BUILD FAILURE | |
| [INFO] ------------------------------------------------------------------------ | |
| [INFO] Total time: 08:19 min | |
| [INFO] Finished at: 2015-01-22T14:45:00-06:00 | |
| [INFO] Final Memory: 65M/1372M | |
| [INFO] ------------------------------------------------------------------------ | |
| [ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0-RC2:test (test) on project adam-cli_2.11: There are test failures -> [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/MojoFailureException | |
| [ERROR] | |
| [ERROR] After correcting the problems, you can resume the build with the command | |
| [ERROR] mvn <goals> -rf :adam-cli_2.11 |
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