gistfile1.txt

[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.11 ---

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (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.

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);devtools::document()
Updating bdgenomics.adam documentation
Loading bdgenomics.adam
Creating a new generic function for 'pipe' in package 'bdgenomics.adam'
Creating a new generic function for 'transform' in package 'bdgenomics.adam'
Creating a new generic function for 'save' in package 'bdgenomics.adam'
Creating a new generic function for 'sort' in package 'bdgenomics.adam'

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, intersect, rank, rbind,
    sample, subset, summary, transform, union

Writing NAMESPACE
Writing ADAMContext.Rd
Writing createADAMContext.Rd
Writing loadAlignments-ADAMContext-character-method.Rd
Writing loadContigFragments-ADAMContext-character-method.Rd
Writing loadFragments-ADAMContext-character-method.Rd
Writing loadFeatures-ADAMContext-character-method.Rd
Writing loadCoverage-ADAMContext-character-method.Rd
Writing loadGenotypes-ADAMContext-character-method.Rd
Writing loadVariants-ADAMContext-character-method.Rd
Writing GenomicDataset.Rd
Writing AlignmentRecordRDD.Rd
Writing CoverageRDD.Rd
Writing FragmentRDD.Rd
Writing toVariantContexts.Rd
Writing toVariants.Rd
Writing NucleotideContigFragmentRDD.Rd
Writing VariantContextRDD.Rd
Writing FeatureRDD.Rd
Writing GenotypeRDD.Rd
Writing VariantRDD.Rd
Writing pipe-GenomicDataset-ANY-character-character-character-method.Rd
Writing cache-GenomicDataset-method.Rd
Writing persist-GenomicDataset-character-method.Rd
Writing unpersist-GenomicDataset-method.Rd
Writing sort-GenomicDataset-method.Rd
Writing sortLexicographically-GenomicDataset-method.Rd
Writing toDF-GenomicDataset-method.Rd
Writing transform-GenomicDataset-function-method.Rd
Writing transmute-GenomicDataset-function-character-method.Rd
Writing broadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing broadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing fullOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing toFragments-AlignmentRecordRDD-method.Rd
Writing saveAsSam-AlignmentRecordRDD-character-method.Rd
Writing toCoverage-AlignmentRecordRDD-method.Rd
Writing save-AlignmentRecordRDD-character-method.Rd
Writing countKmers-AlignmentRecordRDD-numeric-method.Rd
Writing sortReadsByReferencePosition-AlignmentRecordRDD-method.Rd
Writing sortReadsByReferencePositionAndIndex-AlignmentRecordRDD-method.Rd
Writing markDuplicates-AlignmentRecordRDD-method.Rd
Writing recalibrateBaseQualities-AlignmentRecordRDD-VariantRDD-character-method.Rd
Writing realignIndels-AlignmentRecordRDD-method.Rd
Writing save-CoverageRDD-character-method.Rd
Writing collapse-CoverageRDD-method.Rd
Writing toFeatures-CoverageRDD-method.Rd
Writing coverage-CoverageRDD-method.Rd
Writing flatten-CoverageRDD-method.Rd
Writing save-FeatureRDD-character-method.Rd
Writing toCoverage-FeatureRDD-method.Rd
Writing toReads-FragmentRDD-method.Rd
Writing markDuplicates-FragmentRDD-method.Rd
Writing save-FragmentRDD-character-method.Rd
Writing saveAsParquet-GenotypeRDD-character-method.Rd
Writing toVariants-GenotypeRDD-method.Rd
Writing toVariantContexts-GenotypeRDD-method.Rd
Writing save-NucleotideContigFragmentRDD-character-method.Rd
Writing flankAdjacentFragments-NucleotideContigFragmentRDD-numeric-method.Rd
Writing saveAsParquet-VariantRDD-character-method.Rd
Writing toVariantContexts-VariantRDD-method.Rd
Writing saveAsVcf-VariantContextRDD-character-method.Rd
Warning messages:
1: In check_dep_version(pkg, version, compare) :
  Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
2: In check_dep_version(pkg, version, compare) :
  Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
3: package 'SparkR' was built under R version 3.4.4 
> 
> 
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-r) @ adam-r-spark2_2.11 ---
* checking for file 'bdgenomics.adam/DESCRIPTION' ... OK
* preparing 'bdgenomics.adam':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'bdgenomics.adam_0.24.0.tar.gz'
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd'
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd'

[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 /tmp/adamTestChjDfSY/deleteMePleaseThisIsNoLongerNeeded/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 '/tmp/adamTestChjDfSY/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-redhat-linux-gnu (64-bit)
* using session charset: ASCII
* checking for file 'bdgenomics.adam/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bdgenomics.adam' version '0.24.0'
* 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 ... NOTE
Found the following non-portable file paths:
  bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
  bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package 'bdgenomics.adam' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'SparkR' was built under R version 3.4.4
See '/tmp/adamTestChjDfSY/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Duplicated \argument entries in documentation object 'GenomicDataset':
  '...' 'genomicRdd' '...' 'genomicRdd' '...' 'genomicRdd' '...'
  'genomicRdd' '...' 'genomicRdd' '...' 'genomicRdd' '...' 'genomicRdd'
  '...' 'genomicRdd' '...' 'genomicRdd' '...' 'genomicRdd' '...'

Undocumented arguments in documentation object 'toVariants,GenotypeRDD-method'
  'ardd'

Undocumented arguments in documentation object 'toVariants'
  '...'

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 the 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

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  '/tmp/adamTestChjDfSY/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam.Rcheck/00check.log'
for details.