SparkR CRAN check using https://github.com/shivaram/spark-1/tree/sparkr-cran-changes

sparkr-cran-check.txt

* using log directory ‘/Users/shivaram/debian-shared/spark-1/R/SparkR.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-tests --as-cran’
* checking for file ‘SparkR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SparkR’ version ‘2.0.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Shivaram Venkataraman <shivaram@cs.berkeley.edu>’
New submission

Package has FOSS license, installs .class/.jar but has no 'java' directory.
* 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 ‘SparkR’ can be installed ... OK
* 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  window.orderBy window.partitionBy
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following calls to attach():
File ‘SparkR/R/DataFrame.R’:
  attach(newEnv, pos = pos, name = name, warn.conflicts = warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'cache' and siglist 'RDD'
  generic 'collect' and siglist 'RDD'
  generic 'count' and siglist 'RDD'
  generic 'distinct' and siglist 'RDD'
  generic 'first' and siglist 'RDD'
  generic 'join' and siglist 'RDD,RDD'
  generic 'length' and siglist 'RDD'
  generic 'partitionBy' and siglist 'RDD'
  generic 'persist' and siglist 'RDD,character'
  generic 'repartition' and siglist 'RDD'
  generic 'show' and siglist 'RDD'
  generic 'take' and siglist 'RDD,numeric'
  generic 'unpersist' and siglist 'RDD'
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 'add_months'
  ‘y’ ‘x’

Undocumented arguments in documentation object 'alias'
  ‘object’ ‘data’

Undocumented arguments in documentation object 'approxCountDistinct'
  ‘...’ ‘rsd’
Duplicated \argument entries in documentation object 'approxCountDistinct':
  ‘x’

Duplicated \argument entries in documentation object 'arrange':
  ‘x’

Undocumented arguments in documentation object 'as.data.frame'
  ‘row.names’ ‘optional’ ‘...’

Undocumented arguments in documentation object 'avg'
  ‘...’

Undocumented arguments in documentation object 'between'
  ‘x’

Undocumented arguments in documentation object 'bround'
  ‘...’ ‘scale’

Undocumented arguments in documentation object 'cast'
  ‘x’ ‘dataType’

Duplicated \argument entries in documentation object 'coltypes':
  ‘x’

Undocumented arguments in documentation object 'asc'
  ‘x’ ‘...’

Undocumented arguments in documentation object 'colnames'
  ‘do.NULL’ ‘prefix’ ‘value’

Undocumented arguments in documentation object 'concat_ws'
  ‘sep’ ‘x’ ‘...’

Undocumented arguments in documentation object 'conv'
  ‘x’ ‘fromBase’ ‘toBase’

Undocumented arguments in documentation object 'corr'
  ‘...’
Duplicated \argument entries in documentation object 'corr':
  ‘x’

Duplicated \argument entries in documentation object 'countDistinct':
  ‘x’ ‘...’

Undocumented arguments in documentation object 'cov'
  ‘...’
Duplicated \argument entries in documentation object 'cov':
  ‘x’ ‘col1’ ‘col2’

Undocumented arguments in documentation object 'createDataFrame'
  ‘samplingRatio’ ‘x’ ‘...’

Undocumented arguments in documentation object 'createExternalTable'
  ‘...’

Undocumented arguments in documentation object 'crosstab'
  ‘x’

Undocumented arguments in documentation object 'cume_dist'
  ‘x’

Undocumented arguments in documentation object 'date_add'
  ‘y’ ‘x’

Undocumented arguments in documentation object 'date_sub'
  ‘y’ ‘x’

Undocumented arguments in documentation object 'dense_rank'
  ‘x’

Undocumented arguments in documentation object 'drop'
  ‘...’ ‘col’
Documented arguments not in \usage in documentation object 'drop':
  ‘cols’

Undocumented arguments in documentation object 'explain'
  ‘...’

Undocumented arguments in documentation object 'explode'
  ‘x’

Undocumented arguments in documentation object 'expr'
  ‘x’

Undocumented arguments in documentation object 'first'
  ‘na.rm’
Duplicated \argument entries in documentation object 'first':
  ‘x’

Undocumented arguments in documentation object 'fitted'
  ‘...’ ‘method’

Undocumented arguments in documentation object 'format_string'
  ‘format’ ‘x’ ‘...’

Undocumented arguments in documentation object 'from_unixtime'
  ‘x’ ‘...’ ‘format’

Undocumented arguments in documentation object 'gapply'
  ‘...’
Duplicated \argument entries in documentation object 'gapply':
  ‘x’

Undocumented arguments in documentation object 'gapplyCollect'
  ‘...’
Duplicated \argument entries in documentation object 'gapplyCollect':
  ‘x’

Undocumented arguments in documentation object 'glm'
  ‘weights’ ‘subset’ ‘na.action’ ‘start’ ‘etastart’ ‘mustart’ ‘offset’
  ‘control’ ‘model’ ‘method’ ‘x’ ‘y’ ‘contrasts’ ‘...’

Undocumented arguments in documentation object 'group_by'
  ‘...’

Undocumented arguments in documentation object 'hash'
  ‘...’

Undocumented arguments in documentation object 'histogram'
  ‘col’
Documented arguments not in \usage in documentation object 'histogram':
  ‘colname’

Undocumented arguments in documentation object 'ifelse'
  ‘test’ ‘yes’ ‘no’

Undocumented arguments in documentation object 'insertInto'
  ‘...’

Undocumented arguments in documentation object 'lag'
  ‘x’ ‘...’ ‘offset’ ‘defaultValue’

Undocumented arguments in documentation object 'last'
  ‘...’ ‘na.rm’

Undocumented arguments in documentation object 'lead'
  ‘x’ ‘offset’ ‘defaultValue’

Undocumented arguments in documentation object 'lit'
  ‘x’

Undocumented arguments in documentation object 'locate'
  ‘substr’ ‘str’ ‘...’ ‘pos’

Undocumented arguments in documentation object 'lpad'
  ‘x’ ‘len’ ‘pad’

Undocumented arguments in documentation object '%in%'
  ‘x’ ‘table’

Undocumented arguments in documentation object 'merge'
  ‘...’ ‘all’ ‘suffixes’

Undocumented arguments in documentation object 'monotonically_increasing_id'
  ‘x’

Undocumented arguments in documentation object 'mutate'
  ‘...’ ‘_data’
Documented arguments not in \usage in documentation object 'mutate':
  ‘col’

Undocumented arguments in documentation object 'dropna'
  ‘object’ ‘...’
Duplicated \argument entries in documentation object 'dropna':
  ‘x’ ‘cols’

Duplicated \argument entries in documentation object 'n':
  ‘x’

Undocumented arguments in documentation object 'ntile'
  ‘x’

Undocumented arguments in documentation object 'otherwise'
  ‘x’ ‘value’

Undocumented arguments in documentation object 'over'
  ‘x’ ‘window’

Undocumented arguments in documentation object 'partitionBy'
  ‘...’ ‘col’

Undocumented arguments in documentation object 'percent_rank'
  ‘x’

Undocumented arguments in documentation object 'persist'
  ‘newLevel’

Undocumented arguments in documentation object 'posexplode'
  ‘x’

Undocumented arguments in documentation object 'predict'
  ‘object’ ‘...’

Undocumented arguments in documentation object 'rand'
  ‘seed’

Undocumented arguments in documentation object 'randn'
  ‘seed’

Undocumented arguments in documentation object 'rank'
  ‘x’ ‘...’

Undocumented arguments in documentation object 'rbind'
  ‘deparse.level’

Undocumented arguments in documentation object 'read.df'
  ‘...’

Undocumented arguments in documentation object 'read.jdbc'
  ‘...’

Undocumented arguments in documentation object 'read.parquet'
  ‘...’

Undocumented arguments in documentation object 'regexp_extract'
  ‘x’ ‘pattern’ ‘idx’

Undocumented arguments in documentation object 'regexp_replace'
  ‘x’ ‘pattern’ ‘replacement’

Undocumented arguments in documentation object 'repartition'
  ‘...’

Undocumented arguments in documentation object 'rint'
  ‘...’

Undocumented arguments in documentation object 'row_number'
  ‘x’

Undocumented arguments in documentation object 'rpad'
  ‘x’ ‘len’ ‘pad’

Undocumented arguments in documentation object 'saveAsTable'
  ‘...’

Undocumented arguments in documentation object 'sd'
  ‘na.rm’

Undocumented arguments in documentation object 'select'
  ‘...’ ‘name’ ‘value’

Undocumented arguments in documentation object 'setJobGroup'
  ‘groupId’
Documented arguments not in \usage in documentation object 'setJobGroup':
  ‘groupid’

Undocumented arguments in documentation object 'shiftLeft'
  ‘y’ ‘x’

Undocumented arguments in documentation object 'shiftRight'
  ‘y’ ‘x’

Undocumented arguments in documentation object 'shiftRightUnsigned'
  ‘y’ ‘x’

Undocumented arguments in documentation object 'show'
  ‘object’
Documented arguments not in \usage in documentation object 'show':
  ‘x’

Undocumented arguments in documentation object 'showDF'
  ‘...’

Duplicated \argument entries in documentation object 'signum':
  ‘x’

Undocumented arguments in documentation object 'size'
  ‘x’

Undocumented arguments in documentation object 'spark.glm'
  ‘...’

Undocumented arguments in documentation object 'spark.kmeans'
  ‘...’ ‘newData’

Undocumented arguments in documentation object 'spark.naiveBayes'
  ‘...’

Undocumented arguments in documentation object 'spark.survreg'
  ‘...’

Undocumented arguments in documentation object 'sparkR.session'
  ‘...’

Undocumented arguments in documentation object 'spark_partition_id'
  ‘x’

Undocumented arguments in documentation object 'struct'
  ‘...’

Undocumented arguments in documentation object 'structField'
  ‘...’

Undocumented arguments in documentation object '[['
  ‘i’ ‘j’ ‘...’

Undocumented arguments in documentation object 'substr'
  ‘x’

Undocumented arguments in documentation object 'substring_index'
  ‘x’ ‘delim’ ‘count’

Undocumented arguments in documentation object 'agg'
  ‘...’
Duplicated \argument entries in documentation object 'agg':
  ‘x’

Undocumented arguments in documentation object 'describe'
  ‘object’

Undocumented arguments in documentation object 'take'
  ‘x’ ‘num’

Undocumented arguments in documentation object 'translate'
  ‘x’ ‘matchingString’ ‘replaceString’

Undocumented arguments in documentation object 'unix_timestamp'
  ‘x’ ‘format’

Undocumented arguments in documentation object 'var'
  ‘y’ ‘na.rm’ ‘use’

Undocumented arguments in documentation object 'when'
  ‘condition’ ‘value’

Undocumented arguments in documentation object 'window'
  ‘x’ ‘...’ ‘windowDuration’ ‘slideDuration’ ‘startTime’

Undocumented arguments in documentation object 'window.orderBy'
  ‘x’ ‘...’

Undocumented arguments in documentation object 'window.partitionBy'
  ‘x’ ‘...’

Undocumented arguments in documentation object 'write.df'
  ‘...’

Undocumented arguments in documentation object 'write.jdbc'
  ‘...’

Undocumented arguments in documentation object 'write.ml'
  ‘object’ ‘path’ ‘...’

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.
S3 methods shown with full name in documentation object 'window.orderBy':
  ‘window.orderBy’

S3 methods shown with full name in documentation object 'window.partitionBy':
  ‘window.partitionBy’

The \usage entries for S3 methods should use the \method markup and not
their full name.
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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs