[ADAM-1699] Make GenomicRDD.toXxx method names consistent. #1700

heuermh · 2017-08-29T22:59:57Z

AmplabJenkins · 2017-08-29T23:22:52Z

Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 09875798cf5db255e6f31685f9c8b82c8f65cba6 # timeout=10Checking out Revision 09875798cf5db255e6f31685f9c8b82c8f65cba6 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 09875798cf5db255e6f31685f9c8b82c8f65cba6First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

coveralls · 2017-08-29T23:37:33Z

Coverage remained the same at 83.43% when pulling f905d57 on heuermh:genomicrdd-toxxx into 12c56fd on bigdatagenomics:master.

fnothaft

LGTM! Thanks @heuermh!

fnothaft · 2017-08-29T23:41:24Z

I will leave this open for 24hrs, in case anyone else has comments.

coveralls · 2017-08-30T01:54:19Z

Coverage remained the same at 83.43% when pulling b9f094f on heuermh:genomicrdd-toxxx into 12c56fd on bigdatagenomics:master.

AmplabJenkins · 2017-08-30T02:05:31Z

Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 10b6668 # timeout=10Checking out Revision 10b6668 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 10b6668bbc6f0dd8b5c7e2579f06710e8a289abaFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2017-08-30T13:04:17Z

Test FAILed.
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 58f4e209683008bed4488b3959b7a35d15d00b6a # timeout=10Checking out Revision 58f4e209683008bed4488b3959b7a35d15d00b6a (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 58f4e209683008bed4488b3959b7a35d15d00b6aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

coveralls · 2017-08-30T13:44:26Z

Coverage remained the same at 83.593% when pulling 5346666 on heuermh:genomicrdd-toxxx into 511f925 on bigdatagenomics:master.

AmplabJenkins · 2017-08-30T13:53:47Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 979ae565de7a9b0c80eb1c0b6ee863a60d6b29e9 # timeout=10Checking out Revision 979ae565de7a9b0c80eb1c0b6ee863a60d6b29e9 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 979ae565de7a9b0c80eb1c0b6ee863a60d6b29e9First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

coveralls · 2017-08-30T14:15:29Z

Coverage remained the same at 83.593% when pulling 2244520 on heuermh:genomicrdd-toxxx into 511f925 on bigdatagenomics:master.

AmplabJenkins · 2017-08-30T14:25:31Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains ac2fdd4cf3509e8441ed644320a565d5ecf741c1 # timeout=10Checking out Revision ac2fdd4cf3509e8441ed644320a565d5ecf741c1 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ac2fdd4cf3509e8441ed644320a565d5ecf741c1First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

coveralls · 2017-08-30T14:38:04Z

Coverage remained the same at 83.593% when pulling 2244520 on heuermh:genomicrdd-toxxx into 511f925 on bigdatagenomics:master.

AmplabJenkins · 2017-08-30T14:51:16Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 30386964689b05d73be8657a2ac365517de18d2b # timeout=10Checking out Revision 30386964689b05d73be8657a2ac365517de18d2b (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 30386964689b05d73be8657a2ac365517de18d2bFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2017-08-31T21:34:07Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains bf7eb9e # timeout=10Checking out Revision bf7eb9e (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f bf7eb9e > /home/jenkins/git2/bin/git rev-list 30386964689b05d73be8657a2ac365517de18d2b # timeout=10Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

coveralls · 2017-08-31T21:36:17Z

Coverage remained the same at 83.593% when pulling 3e06868 on heuermh:genomicrdd-toxxx into 511f925 on bigdatagenomics:master.

fnothaft · 2017-09-06T06:27:38Z

@heuermh I saw you were making changes to this, so I wanted to wait for you to be done before merging. I see you haven't changed this in a few days; is this good to merge from your side, or do you have more work to do here? If you are done, I will re-review/merge.

heuermh · 2017-09-06T12:00:45Z

Sorry, I haven't been able to pass Jenkins yet.

heuermh · 2017-09-06T15:46:07Z

I tried the adam-r build from this branch on a completely new environment

# Build ADAM assembly jar and set up environment variables

$ ./scripts/move_to_spark_2.sh
$ ./scripts/move_to_scala_2.11.sh
$ mvn clean install
$ export SPARK_HOME=/usr/local/Cellar/apache-spark/2.2.0/libexec
$ export ADAM_HOME=`pwd`
$ export ASSEMBLY_DIR="${ADAM_HOME}/adam-assembly/target"
$ export ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
$ export SPARKR_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} sparkr-shell"

$ env | grep HOME
SPARK_HOME=/usr/local/Cellar/apache-spark/2.2.0/libexec
ADAM_HOME=/Users/heuermh/working/adam
HOME=/Users/heuermh

$ env | grep ASSEMBLY
ASSEMBLY_JAR=adam-assembly-spark2_2.11-0.23.0-SNAPSHOT.jar
ASSEMBLY_DIR=/Users/heuermh/working/adam/adam-assembly/target

$ echo $SPARKR_SUBMIT_ARGS
--jars /Users/heuermh/working/adam/adam-assembly/target/adam-assembly-spark2_2.11-0.23.0-SNAPSHOT.jar --driver-class-path /Users/heuermh/working/adam/adam-assembly/target/adam-assembly-spark2_2.11-0.23.0-SNAPSHOT.jar sparkr-shell


# Install R and libraries

$ brew install r

$ R CMD INSTALL $SPARK_HOME/R/lib/SparkR
installing to library ‘/usr/local/lib/R/3.4/site-library’
installing *binary* package ‘SparkR’ ...
DONE (SparkR)

$ R -e "install.packages('testthat', repos='http://cran.rstudio.com/')"
...
installing to /usr/local/lib/R/3.4/site-library/testthat/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (testthat)


# Build ADAM with R profile enabled

$ mvn -Pr package
[INFO] Scanning for projects...
...
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: R APIs 0.23.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-r-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-r-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-r-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/heuermh/working/adam/adam-r/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-r) @ adam-r-spark2_2.11 ---
* checking for file ‘bdg.adam/DESCRIPTION’ ... OK
* preparing ‘bdg.adam’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘bdg.adam_0.23.0.tar.gz’

[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/heuermh/working/adam/adam-r/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-r) @ adam-r-spark2_2.11 ---
* using log directory ‘/Users/heuermh/working/adam/adam-r/bdg.adam.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘bdg.adam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bdg.adam’ version ‘0.23.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bdg.adam’ can be installed ... ERROR
Installation failed.
See ‘/Users/heuermh/working/adam/adam-r/bdg.adam.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/Users/heuermh/working/adam/adam-r/bdg.adam.Rcheck/00check.log’
for details.

[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
	at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
	at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:764)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:711)
	at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:289)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:154)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:146)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:309)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:194)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:107)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:993)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:345)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:191)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [ 11.473 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  5.222 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [05:15 min]
[INFO] ADAM_2.11: APIs for Java ........................... SUCCESS [ 13.573 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 45.822 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 10.685 s]
[INFO] ADAM_2.11: R APIs .................................. FAILURE [  8.391 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:51 min
[INFO] Finished at: 2017-09-06T10:32:05-05:00
[INFO] Final Memory: 46M/434M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-r) on project adam-r-spark2_2.11: Command execution failed.: Process exited with an error: 1 (Exit value: 1) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :adam-r-spark2_2.11

$ cat /Users/heuermh/working/adam/adam-r/bdg.adam.Rcheck/00install.out 
* installing *source* package ‘bdg.adam’ ...
** R
** preparing package for lazy loading
Creating a new generic function for ‘pipe’ in package ‘bdg.adam’
Creating a new generic function for ‘transform’ in package ‘bdg.adam’
Creating a new generic function for ‘save’ in package ‘bdg.adam’
Creating a new generic function for ‘sort’ in package ‘bdg.adam’
** help
No man pages found in package  ‘bdg.adam’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: no function found corresponding to methods exports from ‘bdg.adam’ for: ‘toFeatureRDD’
Error: package or namespace load failed for ‘bdg.adam’ in loadNamespace(package, lib.loc):
 in ‘bdg.adam’ methods for export not found: toFeatureRDD
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/heuermh/working/adam/adam-r/bdg.adam.Rcheck/bdg.adam’

$ find . -name "*.R" | xargs grep toFeatureRDD

$ find . -name "*.R" | xargs grep toFeatures
./adam-r/bdg.adam/R/generics.R:setGeneric("toFeatures",
./adam-r/bdg.adam/R/generics.R:           function(ardd) { standardGeneric("toFeatures") })
./adam-r/bdg.adam/R/rdd.R:setMethod("toFeatures", signature(ardd = "CoverageRDD"),
./adam-r/bdg.adam/R/rdd.R:              FeatureRDD(sparkR.callJMethod(ardd@jrdd, "toFeatures"))

There are no references to toFeatureRDD. What am I missing?

pbashyal-nmdp · 2017-09-06T16:10:14Z

The NAMESPACE file says the package exports toFeatureRDD. See

adam/adam-r/bdg.adam/NAMESPACE

Line 31 in 28bbb48

exportMethods(toFeatureRDD)

You need your functions that are exported to be in NAMESPACE, otherwise they are internal to the package. I don't see any changes to NAMESPACE. If you use devtools::document() to generate the documentation, it will update the NAMESPACE file properly as well.

heuermh · 2017-09-06T16:21:39Z

I see, thanks! So I have to get the prereqs working for #1672 then.

Is there any reason to commit NAMESPACE to git if it is supposed to be generated by roxygen2? Or alternatively, if at least one of us has that process working, should we commit all the generated docs (NAMESPACE and man directory) to git?

pbashyal-nmdp · 2017-09-06T17:05:54Z

Yes, you would want NAMESPACE to be checked in. It's easier to use roxygen2 to generate it rather than manually. The package build step requires the NAMESPACE even if you don't generate the help files. I see the man folder checked in R packages online, so I think that's reasonable.

fnothaft · 2017-09-06T17:29:51Z

+1 @pbashyal-nmdp.

heuermh · 2017-09-06T18:20:07Z

Welcome back!

After the OS upgrade, I can build roxygen2 and devtools. It reports a couple warnings, I'll try to fix those

$ R -e "library(devtools);document()"

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(devtools);document()
Updating bdg.adam documentation
Loading bdg.adam
Loading required package: SparkR

Attaching package: ‘SparkR’

The following objects are masked from ‘package:stats’:

    cov, filter, lag, na.omit, predict, sd, var, window

The following objects are masked from ‘package:base’:

    as.data.frame, colnames, colnames<-, drop, endsWith, intersect,
    rank, rbind, sample, startsWith, subset, summary, transform, union

Creating a new generic function for ‘pipe’ in package ‘bdg.adam’
Creating a new generic function for ‘transform’ in package ‘bdg.adam’
Creating a new generic function for ‘save’ in package ‘bdg.adam’
Creating a new generic function for ‘sort’ in package ‘bdg.adam’
Writing NAMESPACE
Writing ADAMContext-class.Rd
...
Warning messages:
1: toVariantContexts-GenotypeRDD-method.Rd is missing name/title. Skipping 
2: toVariantContexts-VariantRDD-method.Rd is missing name/title. Skipping

heuermh · 2017-09-06T18:26:15Z

Fixed the warnings. bdg.adam/man is currently .gitignored. Should I fix that and git add the man directory in this pull request?

pbashyal-nmdp · 2017-09-06T18:32:43Z

Yes, I suggest adding man directory.

AmplabJenkins · 2017-09-06T18:50:45Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2358/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 5ff669791cba41809f2ffdc545d389fb76a4a3d0 # timeout=10Checking out Revision 5ff669791cba41809f2ffdc545d389fb76a4a3d0 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 5ff669791cba41809f2ffdc545d389fb76a4a3d0 > /home/jenkins/git2/bin/git rev-list bf7eb9e # timeout=10Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2017-09-06T21:18:42Z

Spark 2.x Scala 2.11 works fine for me locally

...
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-r) @ adam-r-spark2_2.11 ---
* checking for file ‘bdg.adam/DESCRIPTION’ ... OK
* preparing ‘bdg.adam’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘bdg.adam_0.23.0.tar.gz’

[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory working/adam/adam-r/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-r) @ adam-r-spark2_2.11 ---
* using log directory ‘working/adam/adam-r/bdg.adam.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘bdg.adam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bdg.adam’ version ‘0.23.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bdg.adam’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘SparkR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ADAMContext: no visible global function definition for
  ‘sparkR.callJMethod’
ADAMContext: no visible global function definition for
  ‘sparkR.newJObject’
ADAMContext: no visible global function definition for ‘new’
AlignmentRecordRDD: no visible global function definition for ‘new’
CoverageRDD: no visible global function definition for ‘new’
FeatureRDD: no visible global function definition for ‘new’
FragmentRDD: no visible global function definition for ‘new’
GenotypeRDD: no visible global function definition for ‘new’
NucleotideContigFragmentRDD: no visible global function definition for
  ‘new’
VariantContextRDD: no visible global function definition for ‘new’
VariantRDD: no visible global function definition for ‘new’
aggregatedCoverage,CoverageRDD: no visible global function definition
  for ‘sparkR.callJMethod’
collapse,CoverageRDD: no visible global function definition for
  ‘sparkR.callJMethod’
countKmers,AlignmentRecordRDD-numeric: no visible global function
  definition for ‘new’
countKmers,AlignmentRecordRDD-numeric: no visible global function
  definition for ‘sparkR.callJMethod’
coverage,CoverageRDD: no visible global function definition for
  ‘sparkR.callJMethod’
flankAdjacentFragments,NucleotideContigFragmentRDD-numeric: no visible
  global function definition for ‘sparkR.callJMethod’
flatten,CoverageRDD: no visible global function definition for
  ‘sparkR.callJMethod’
loadAlignments,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
loadContigFragments,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
loadCoverage,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
loadFeatures,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
loadFragments,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
loadGenotypes,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
loadVariants,ADAMContext-character: no visible global function
  definition for ‘sparkR.callJMethod’
markDuplicates,AlignmentRecordRDD: no visible global function
  definition for ‘sparkR.callJMethod’
markDuplicates,FragmentRDD: no visible global function definition for
  ‘sparkR.callJMethod’
pipe,GenomicRDD-character-character-character-character: no visible
  global function definition for ‘sparkR.callJStatic’
pipe,GenomicRDD-character-character-character-character: no visible
  global function definition for ‘sparkR.callJMethod’
realignIndels,AlignmentRecordRDD-ANY: no visible global function
  definition for ‘sparkR.callJStatic’
realignIndels,AlignmentRecordRDD-ANY: no visible global function
  definition for ‘sparkR.callJMethod’
realignIndels,AlignmentRecordRDD-VariantRDD: no visible global function
  definition for ‘sparkR.callJStatic’
realignIndels,AlignmentRecordRDD-VariantRDD: no visible global function
  definition for ‘sparkR.callJMethod’
recalibrateBaseQualities,AlignmentRecordRDD-VariantRDD-character: no
  visible global function definition for ‘sparkR.callJStatic’
recalibrateBaseQualities,AlignmentRecordRDD-VariantRDD-character: no
  visible global function definition for ‘sparkR.callJMethod’
save,AlignmentRecordRDD-character: no visible global function
  definition for ‘sparkR.callJMethod’
save,CoverageRDD-character: no visible global function definition for
  ‘sparkR.callJMethod’
save,FeatureRDD-character: no visible global function definition for
  ‘sparkR.callJMethod’
save,FragmentRDD-character: no visible global function definition for
  ‘sparkR.callJMethod’
save,NucleotideContigFragmentRDD-character: no visible global function
  definition for ‘sparkR.callJMethod’
saveAsParquet,GenotypeRDD-character: no visible global function
  definition for ‘sparkR.callJMethod’
saveAsParquet,VariantRDD-character: no visible global function
  definition for ‘sparkR.callJMethod’
saveAsSam,AlignmentRecordRDD-character: no visible global function
  definition for ‘sparkR.callJStatic’
saveAsSam,AlignmentRecordRDD-character: no visible global function
  definition for ‘sparkR.callJMethod’
saveAsVcf,VariantContextRDD-character: no visible global function
  definition for ‘sparkR.callJStatic’
saveAsVcf,VariantContextRDD-character: no visible global function
  definition for ‘sparkR.callJMethod’
sort,GenomicRDD: no visible global function definition for
  ‘sparkR.callJMethod’
sortLexicographically,GenomicRDD: no visible global function definition
  for ‘sparkR.callJMethod’
sortReadsByReferencePosition,AlignmentRecordRDD: no visible global
  function definition for ‘sparkR.callJMethod’
sortReadsByReferencePositionAndIndex,AlignmentRecordRDD: no visible
  global function definition for ‘sparkR.callJMethod’
toCoverage,AlignmentRecordRDD: no visible global function definition
  for ‘sparkR.callJMethod’
toCoverage,FeatureRDD: no visible global function definition for
  ‘sparkR.callJMethod’
toDF,GenomicDataset: no visible global function definition for
  ‘sparkR.callJMethod’
toDF,GenomicDataset: no visible global function definition for ‘new’
toFeatures,CoverageRDD: no visible global function definition for
  ‘sparkR.callJMethod’
toFragments,AlignmentRecordRDD: no visible global function definition
  for ‘sparkR.callJMethod’
toReads,FragmentRDD: no visible global function definition for
  ‘sparkR.callJMethod’
toVariantContexts,GenotypeRDD: no visible global function definition
  for ‘sparkR.callJMethod’
toVariantContexts,VariantRDD: no visible global function definition for
  ‘sparkR.callJMethod’
transform,GenomicRDD-function: no visible global function definition
  for ‘sparkR.callJMethod’
transmute,GenomicRDD-function-character: no visible global function
  definition for ‘sparkR.callJStatic’
transmute,GenomicRDD-function-character: no visible global function
  definition for ‘new’
transmute,GenomicRDD-function-character: no visible global function
  definition for ‘sparkR.callJMethod’
wrapTransformation,GenomicRDD-function: no visible global function
  definition for ‘sparkR.callJStatic’
Undefined global functions or variables:
  new sparkR.callJMethod sparkR.callJStatic sparkR.newJObject
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘ADAMContext’ ‘aggregatedCoverage’ ‘collapse’ ‘countKmers’ ‘coverage’
  ‘flankAdjacentFragments’ ‘flatten’ ‘loadAlignments’
  ‘loadContigFragments’ ‘loadCoverage’ ‘loadFeatures’ ‘loadFragments’
  ‘loadGenotypes’ ‘loadVariants’ ‘markDuplicates’ ‘pipe’
  ‘realignIndels’ ‘recalibrateBaseQualities’ ‘save’ ‘saveAsParquet’
  ‘saveAsSam’ ‘saveAsVcf’ ‘sort’ ‘sortLexicographically’
  ‘sortReadsByReferencePosition’ ‘sortReadsByReferencePositionAndIndex’
  ‘toCoverage’ ‘toDF’ ‘toFeatures’ ‘toFragments’ ‘toReads’
  ‘toVariantContexts’ ‘transform’ ‘transmute’
Undocumented S4 classes:
  ‘CoverageRDD’ ‘AlignmentRecordRDD’ ‘NucleotideContigFragmentRDD’
  ‘GenomicDataset’ ‘FragmentRDD’ ‘VariantContextRDD’ ‘VariantRDD’
  ‘GenotypeRDD’ ‘GenomicRDD’ ‘FeatureRDD’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'aggregatedCoverage,CoverageRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'collapse,CoverageRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'countKmers,AlignmentRecordRDD,numeric-method'
  ‘ardd’

Undocumented arguments in documentation object 'coverage,CoverageRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'flankAdjacentFragments,NucleotideContigFragmentRDD,numeric-method'
  ‘ardd’

Undocumented arguments in documentation object 'flatten,CoverageRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'markDuplicates,AlignmentRecordRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'markDuplicates,FragmentRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'pipe,GenomicRDD,character,character,character,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'realignIndels,AlignmentRecordRDD,ANY-method'
  ‘ardd’ ‘maxIndelSize’
Documented arguments not in \usage in documentation object 'realignIndels,AlignmentRecordRDD,ANY-method':
  ‘int’

Undocumented arguments in documentation object 'realignIndels,AlignmentRecordRDD,VariantRDD-method'
  ‘ardd’ ‘maxIndelSize’
Documented arguments not in \usage in documentation object 'realignIndels,AlignmentRecordRDD,VariantRDD-method':
  ‘int’

Undocumented arguments in documentation object 'recalibrateBaseQualities,AlignmentRecordRDD,VariantRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'save,AlignmentRecordRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'save,CoverageRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'save,FeatureRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'save,FragmentRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'save,NucleotideContigFragmentRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'saveAsParquet,GenotypeRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'saveAsParquet,VariantRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'saveAsSam,AlignmentRecordRDD,character-method'
  ‘ardd’

Undocumented arguments in documentation object 'saveAsVcf,VariantContextRDD,character-method'
  ‘ardd’ ‘disableFastConcat’
Documented arguments not in \usage in documentation object 'saveAsVcf,VariantContextRDD,character-method':
  ‘disableFastConcat:’

Undocumented arguments in documentation object 'sort,GenomicRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'sortLexicographically,GenomicRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'sortReadsByReferencePosition,AlignmentRecordRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'sortReadsByReferencePositionAndIndex,AlignmentRecordRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toCoverage,AlignmentRecordRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toCoverage,FeatureRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toFeatures,CoverageRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toFragments,AlignmentRecordRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toReads,FragmentRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toVariantContexts,GenotypeRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toVariantContexts,VariantRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'transform,GenomicRDD,function-method'
  ‘ardd’

Undocumented arguments in documentation object 'transmute,GenomicRDD,function,character-method'
  ‘ardd’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘working/adam/adam-r/bdg.adam.Rcheck/00check.log’
for details.

pbashyal-nmdp · 2017-09-07T18:35:55Z

I've seen Rd files in man directory checked into the repository for R packages. Eg. roxygen2 https://github.com/klutometis/roxygen and devtools https://github.com/hadley/devtools

heuermh · 2017-09-07T18:47:48Z

... and they're not critical for building in the way that the NAMESPACE file is.

I'm not sure about that, the Jenkins build kept failing until I checked them in.

And now that scripts/jenkins-test uses conda and library path stuff for the python and R builds, I'm not sure if I should try to run it locally. If the Jenkins build hadn't passed this morning, I was going to spin up an EC2 instance and try running there.

What we should have is a .gitignore in adam-r that contains !bdg.adam. Can you add that here in a separate commit?

I added !bdg.adam to the .gitignore at the project root, I suppose it would still work at adam-r.

It can't be at adam-r/bdg.adam or Rcheck will complain (see commit 758dfe1).

fnothaft · 2017-09-07T18:59:52Z

... and they're not critical for building in the way that the NAMESPACE file is.

I'm not sure about that, the Jenkins build kept failing until I checked them in.

Hmm, odd. Can you point me at a build where this was failing?

I added !bdg.adam to the .gitignore at the project root, I suppose it would still work at adam-r.

Ah, I hadn't seen you make that add. I'm OK with it at the project root.

heuermh · 2017-09-07T19:46:24Z

This is the most recent failed Jenkins build
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2358/

but whatever error message(s) Rcheck provided are lost when the stuff in /tmp is deleted

* checking whether package 'bdg.adam' can be installed ... ERROR
Installation failed.
See '/tmp/adamTestBpGEYH9/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdg.adam.Rcheck/00install.out' for details.

coveralls · 2017-09-08T13:54:44Z

Coverage decreased (-0.5%) to 83.05% when pulling 1252518 on heuermh:genomicrdd-toxxx into 28bbb48 on bigdatagenomics:master.

coveralls · 2017-09-08T13:54:45Z

Coverage decreased (-0.01%) to 83.534% when pulling 1252518 on heuermh:genomicrdd-toxxx into 28bbb48 on bigdatagenomics:master.

AmplabJenkins · 2017-09-08T14:05:24Z

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2360/
Test PASSed.

fnothaft · 2017-09-12T17:50:59Z

@heuermh can you push a commit that:

Removes the generated R docs
Disable -e right before running the R CMD INSTALL
Cat bdg.adam.Rcheck/00install.out

AmplabJenkins · 2017-09-18T17:24:59Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2382/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 9a742bfe92342744df9af9b2f1fa2197105ebe07 # timeout=10Checking out Revision 9a742bfe92342744df9af9b2f1fa2197105ebe07 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9a742bfe92342744df9af9b2f1fa2197105ebe07 > /home/jenkins/git2/bin/git rev-list b0a9d9e # timeout=10Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2017-09-18T17:31:28Z

@fnothaft Not sure what is going on with the Jenkins builds here. Perhaps I borked something when rebasing?

fnothaft · 2017-09-18T20:12:42Z

Can you make sure you've picked up the Spark 2.2/Hadoop 2.7 build changes?

AmplabJenkins · 2017-09-18T21:14:29Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2383/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 05ecc00d7310b13f72b833b4933bfb3cd6c78845 # timeout=10Checking out Revision 05ecc00d7310b13f72b833b4933bfb3cd6c78845 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 05ecc00d7310b13f72b833b4933bfb3cd6c78845 > /home/jenkins/git2/bin/git rev-list 9a742bfe92342744df9af9b2f1fa2197105ebe07 # timeout=10Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2017-09-18T21:24:16Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2384/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1700/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains a31f864 # timeout=10Checking out Revision a31f864 (origin/pr/1700/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a31f864 > /home/jenkins/git2/bin/git rev-list 05ecc00d7310b13f72b833b4933bfb3cd6c78845 # timeout=10Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2017-09-19T16:57:09Z

Jenkins, retest this please.

AmplabJenkins · 2017-09-19T17:20:02Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2387/
Test PASSed.

heuermh · 2017-09-19T17:32:50Z

I'm going to squash all but the jenkins-test changes into a single commit and hope for the best.

AmplabJenkins · 2017-09-19T18:09:44Z

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2389/
Test PASSed.

fnothaft · 2017-09-22T05:45:56Z

Jenkins, retest this please.

AmplabJenkins · 2017-09-22T06:10:21Z

Test PASSed.
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Test PASSed.

fnothaft · 2017-09-22T06:16:11Z

Merged! Thanks @heuermh!

fnothaft approved these changes Aug 29, 2017

View reviewed changes

heuermh force-pushed the genomicrdd-toxxx branch from a728296 to 5346666 Compare August 30, 2017 13:29

heuermh modified the milestone: 0.23.0 Sep 1, 2017

heuermh force-pushed the genomicrdd-toxxx branch from 99d4d8e to 1252518 Compare September 8, 2017 13:38

heuermh force-pushed the genomicrdd-toxxx branch from 1252518 to 4e3d074 Compare September 18, 2017 17:00

heuermh force-pushed the genomicrdd-toxxx branch from 4e3d074 to 1e1df30 Compare September 18, 2017 21:08

Make GenomicRDD.toXxx method names consistent.

a0bd2dd

heuermh force-pushed the genomicrdd-toxxx branch from 2db0abd to a0bd2dd Compare September 19, 2017 17:34

fnothaft approved these changes Sep 22, 2017

View reviewed changes

fnothaft merged commit ccb2638 into bigdatagenomics:master Sep 22, 2017

heuermh deleted the genomicrdd-toxxx branch September 22, 2017 13:55

fnothaft added a commit to fnothaft/avocado that referenced this pull request Sep 26, 2017

Update for breaking changes from bigdatagenomics/adam#1700.

c0f982e

fnothaft added a commit to bigdatagenomics/avocado that referenced this pull request Sep 26, 2017

Update for breaking changes from bigdatagenomics/adam#1700.

d6bcfe2

[ADAM-1699] Make GenomicRDD.toXxx method names consistent. #1700

[ADAM-1699] Make GenomicRDD.toXxx method names consistent. #1700

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