CRAN Package Check Results for Package HadoopStreaming

Last updated on 2020-09-19 11:50:56 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2 1.86 19.55 21.41 NOTE
r-devel-linux-x86_64-debian-gcc 0.2 1.71 15.67 17.38 NOTE
r-devel-linux-x86_64-fedora-clang 0.2 35.74 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2 27.54 NOTE
r-devel-windows-ix86+x86_64 0.2 4.00 32.00 36.00 ERROR
r-patched-linux-x86_64 0.2 1.93 19.52 21.45 NOTE
r-patched-solaris-x86 0.2 42.10 NOTE
r-release-linux-x86_64 0.2 1.77 19.81 21.58 NOTE
r-release-macos-x86_64 0.2 NOTE
r-release-windows-ix86+x86_64 0.2 4.00 30.00 34.00 ERROR
r-oldrel-macos-x86_64 0.2 NOTE
r-oldrel-windows-ix86+x86_64 0.2 3.00 35.00 38.00 ERROR

Check Details

Version: 0.2
Check: R code for possible problems
Result: NOTE
    hsTableReader: no visible global function definition for 'object.size'
    hsWriteTable: no visible global function definition for 'write.table'
    Undefined global functions or variables:
     object.size write.table
    Consider adding
     importFrom("utils", "object.size", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2
Check: Rd line widths
Result: NOTE
    Rd file 'hsKeyValReader.Rd':
     \usage lines wider than 90 characters:
     hsKeyValReader(file = "", chunkSize = -1, skip = 0, sep = "\t",FUN = function(k, v) cat(paste(k, v, sep = ": "), sep = "\n"))
    
    Rd file 'hsLineReader.Rd':
     \examples lines wider than 100 characters:
     str <- "Hello here are some\nlines of text\nto read in, chunkSize\nlines at a time.\nHow interesting.\nhuh?"
    
    Rd file 'hsTableReader.Rd':
     \examples lines wider than 100 characters:
     str <- "key1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey2\t9.9\nkey2\t10.1\nkey3\t1.0\nkey3\t3.4\nkey4\t9.4\n"
     hsTableReader(con,cols,chunkSize=5,FUN=reducerFullKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)
     hsTableReader(con,cols,chunkSize=6,FUN=reducerKeyAtOnce,ignoreKey=FALSE,singleKey=TRUE,PFUN=reducerPartialKey)
     hsTableReader(con,cols,chunkSize=6,FUN=reducerManyCompleteKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'datafile.txt'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.2
Check: examples
Result: ERROR
    Running examples in 'HadoopStreaming-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HadoopStreaming-package
    > ### Title: Functions facilitating Hadoop streaming with R.
    > ### Aliases: HadoopStreaming-package HadoopStreaming
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > ## STEP 1: MAKE A CONNECTION
    >
    > ## To read from STDIN (used for deployment in Hadoop streaming and for command line testing)
    > con = file(description="stdin",open="r")
    >
    > ## Reading from a text string: useful for very small test examples
    > str <- "Key1\tVal1\nKey2\tVal2\nKey3\tVal3\n"
    > cat(str)
    Key1 Val1
    Key2 Val2
    Key3 Val3
    > con <- textConnection(str, open = "r")
    >
    > ## Reading from a file: useful for testing purposes during development
    > cat(str,file="datafile.txt") # write datafile.txt data in str
    > con <- file("datafile.txt",open="r")
    >
    > ## To get the first few lines of a file (also very useful for testing)
    > numlines = 2
    > con <- pipe(paste("head -n",numlines,'datafile.txt'), "r")
    >
    > ## STEP 2: Write map and reduce scripts, call them mapper.R and
    > ## reducer.R. Alternatively, write a single script taking command line
    > ## flags specifying whether it should run as a mapper or reducer. The
    > ## hsCmdLineArgs function can assist with this.
    > ## Writing #!/usr/bin/env Rscript can make an R file executable from the command line.
    >
    > ## STEP 3a: Running on command line with separate mappers and reducers
    > ## cat inputFile | Rscript mapper.R | sort | Rscript reducer.R
    > ## OR
    > ## cat inputFile | R --vanilla --slave -f mapper.R | sort | R --vanilla --slave -f reducer.R
    >
    > ## STEP 3b: Running on command line with the recommended single file
    > ## approach using Rscript and the hsCmdLineArgs for argument parsing.
    > ## cat inputFile | ./mapReduce.R --mapper | sort | ./mapReduce.R --reducer
    >
    > ## STEP 3c: Running in Hadoop -- Assuming mapper.R and reducer.R can
    > ## run on each computer in the cluster:
    > ## $HADOOP_HOME/bin/hadoop $HADOOP_HOME/contrib/streaming/hadoop-0.19.0-streaming.jar \
    > ## -input inpath -output outpath -mapper \
    > ## "R --vanilla --slave -f mapper.R" -reducer "R --vanilla --slave -f reducer.R" \
    > ## -file ./mapper.R -file ./reducer.R
    >
    > ## STEP 3d: Running in Hadoop, with the recommended single file method:
    > ## $HADOOP_HOME/bin/hadoop $HADOOP_HOME/contrib/streaming/hadoop-0.19.0-streaming.jar \
    > ## -input inpath -output outpath -mapper \
    > ## "mapReduce.R --mapper" -reducer "mapReduce.R --reducer" \
    > ## -file ./mapReduce.R
    >
    >
    >
    > cleanEx()
    Warning in .Internal(gc(verbose, reset, full)) :
     closing unused connection 5 (datafile.txt)
    Warning in .Internal(gc(verbose, reset, full)) :
     closing unused connection 3 (stdin)
    Error: connections left open:
     head -n 2 datafile.txt (pipe)
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2
Check: examples
Result: ERROR
    Running examples in 'HadoopStreaming-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HadoopStreaming-package
    > ### Title: Functions facilitating Hadoop streaming with R.
    > ### Aliases: HadoopStreaming-package HadoopStreaming
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > ## STEP 1: MAKE A CONNECTION
    >
    > ## To read from STDIN (used for deployment in Hadoop streaming and for command line testing)
    > con = file(description="stdin",open="r")
    >
    > ## Reading from a text string: useful for very small test examples
    > str <- "Key1\tVal1\nKey2\tVal2\nKey3\tVal3\n"
    > cat(str)
    Key1 Val1
    Key2 Val2
    Key3 Val3
    > con <- textConnection(str, open = "r")
    >
    > ## Reading from a file: useful for testing purposes during development
    > cat(str,file="datafile.txt") # write datafile.txt data in str
    > con <- file("datafile.txt",open="r")
    >
    > ## To get the first few lines of a file (also very useful for testing)
    > numlines = 2
    > con <- pipe(paste("head -n",numlines,'datafile.txt'), "r")
    >
    > ## STEP 2: Write map and reduce scripts, call them mapper.R and
    > ## reducer.R. Alternatively, write a single script taking command line
    > ## flags specifying whether it should run as a mapper or reducer. The
    > ## hsCmdLineArgs function can assist with this.
    > ## Writing #!/usr/bin/env Rscript can make an R file executable from the command line.
    >
    > ## STEP 3a: Running on command line with separate mappers and reducers
    > ## cat inputFile | Rscript mapper.R | sort | Rscript reducer.R
    > ## OR
    > ## cat inputFile | R --vanilla --slave -f mapper.R | sort | R --vanilla --slave -f reducer.R
    >
    > ## STEP 3b: Running on command line with the recommended single file
    > ## approach using Rscript and the hsCmdLineArgs for argument parsing.
    > ## cat inputFile | ./mapReduce.R --mapper | sort | ./mapReduce.R --reducer
    >
    > ## STEP 3c: Running in Hadoop -- Assuming mapper.R and reducer.R can
    > ## run on each computer in the cluster:
    > ## $HADOOP_HOME/bin/hadoop $HADOOP_HOME/contrib/streaming/hadoop-0.19.0-streaming.jar \
    > ## -input inpath -output outpath -mapper \
    > ## "R --vanilla --slave -f mapper.R" -reducer "R --vanilla --slave -f reducer.R" \
    > ## -file ./mapper.R -file ./reducer.R
    >
    > ## STEP 3d: Running in Hadoop, with the recommended single file method:
    > ## $HADOOP_HOME/bin/hadoop $HADOOP_HOME/contrib/streaming/hadoop-0.19.0-streaming.jar \
    > ## -input inpath -output outpath -mapper \
    > ## "mapReduce.R --mapper" -reducer "mapReduce.R --reducer" \
    > ## -file ./mapReduce.R
    >
    >
    >
    > cleanEx()
    Warning in .Internal(gc(verbose, reset, full)) :
     closing unused connection 5 (datafile.txt)
    Warning in .Internal(gc(verbose, reset, full)) :
     closing unused connection 3 (stdin)
    Error: connections left open:
     head -n 2 datafile.txt (pipe)
    Execution halted
    head: write error
Flavor: r-release-windows-ix86+x86_64