CRAN Package Check Results for Package CINOEDV

Last updated on 2018-02-24 22:47:21 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0 3.44 43.23 46.67 ERROR
r-devel-linux-x86_64-debian-gcc 2.0 3.93 34.21 38.14 ERROR
r-devel-linux-x86_64-fedora-clang 2.0 420.98 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0 415.92 NOTE
r-devel-windows-ix86+x86_64 2.0 11.00 469.00 480.00 NOTE
r-patched-linux-x86_64 2.0 2.75 52.18 54.93 ERROR
r-patched-solaris-x86 2.0 472.80 NOTE
r-release-linux-x86_64 2.0 2.63 51.54 54.17 ERROR
r-release-windows-ix86+x86_64 2.0 12.00 477.00 489.00 NOTE
r-release-osx-x86_64 2.0 NOTE
r-oldrel-windows-ix86+x86_64 2.0 6.00 426.00 432.00 NOTE
r-oldrel-osx-x86_64 2.0 NOTE

Check Details

Version: 2.0
Check: R code for possible problems
Result: NOTE
    BatCINOEDV: no visible global function definition for ‘graphics.off’
    CoInformation: no visible global function definition for ‘combn’
    CombinationEntropy: no visible global function definition for ‘hist’
    ConstructCompleteGraph: no visible global function definition for
     ‘dev.new’
    ConstructCompleteGraph: no visible global function definition for ‘par’
    ConstructCompleteGraph: no visible global function definition for
     ‘plot’
    DegreeAnalysis: no visible global function definition for ‘dev.new’
    DegreeAnalysis: no visible global function definition for ‘hist’
    DegreeAnalysis: no visible global function definition for ‘title’
    ExhaustiveSearch: no visible global function definition for ‘combn’
    HeatMapFactor: no visible global function definition for ‘dev.new’
    InstallPackage: no visible global function definition for
     ‘install.packages’
    NormalizationEffect: no visible global function definition for
     ‘dev.new’
    NormalizationEffect: no visible global function definition for ‘layout’
    NormalizationEffect: no visible global function definition for ‘plot’
    NormalizationEffect: no visible global function definition for ‘lines’
    PSOSearch: no visible global function definition for ‘combn’
    PSOSearch: no visible global function definition for ‘runif’
    PlotTopEffects: no visible global function definition for ‘dev.new’
    PlotTopEffects: no visible global function definition for ‘par’
    PlotTopEffects: no visible global function definition for ‘layout’
    PlotTopEffects: no visible global function definition for ‘barplot’
    PlotTopEffects: no visible global function definition for ‘rainbow’
    PlotTopEffects: no visible global function definition for ‘title’
    Undefined global functions or variables:
     barplot combn dev.new graphics.off hist install.packages layout lines
     par plot rainbow runif title
    Consider adding
     importFrom("grDevices", "dev.new", "graphics.off", "rainbow")
     importFrom("graphics", "barplot", "hist", "layout", "lines", "par",
     "plot", "title")
     importFrom("stats", "runif")
     importFrom("utils", "combn", "install.packages")
    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-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.0
Check: examples
Result: ERROR
    Running examples in ‘CINOEDV-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: BatCINOEDV
    > ### Title: Batch mode for using CINOEDV
    > ### Aliases: BatCINOEDV
    >
    > ### ** Examples
    >
    > File1 <- system.file("extdata","test.mat",package="CINOEDV")
    > File2 <- system.file("extdata","test1.mat",package="CINOEDV")
    > File3 <- system.file("extdata","test1_Name.mat",package="CINOEDV")
    > FileName <- c(File1,File2)
    > SNFName <- c(NA,File3)
    > MaxOrder <- 2
    > RThreshold <- c(1, 1)
    > NThreshold <- c(10, 10)
    > measure <- 1
    > Stra <- 1
    > Pop <- 10
    > Iter <- 10
    > BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure, Stra, Pop, Iter, SNFName)
     The Maximum order : 2
    
     The RatioThreshold : 1 1
    
     The NumberThreshold : 10 10
    
     The input file is : /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/CINOEDV/extdata/test.mat
     Samples: 4000
     Cases: 2000
     Controls: 2000
     SNPs: 10
    
     The SNP Name File : NA
    
    #### Search Results ####
    
     Please waiting for the search ...
     Exhaustive Search !
    
     1-order effect computing ...
    elapsed
     0.048
     2-order effect computing ...
    elapsed
     0.426
    #### Normalization ####
    #### SNP Name Notation ####
    #### Collect Vertices and Edges ####
    #### Construct Complete Graph ####
    dev.new(): using pdf(file="Rplots1.pdf")
    #### Plot Top Effects ####
    dev.new(): using pdf(file="Rplots2.pdf")
    #### Degree Analysis ####
    dev.new(): using pdf(file="Rplots3.pdf")
     SNP Degree
     [1,] "5" "4"
     [2,] "4" "3"
     [3,] "7" "3"
     [4,] "10" "3"
     [5,] "8" "2"
     [6,] "1" "2"
     [7,] "6" "2"
     [8,] "3" "1"
     [9,] "2" "0"
    [10,] "9" "0"
    #### Split subgraphs ####
    dev.new(): using pdf(file="Rplots4.pdf")
    [2018-02-23 04:38:50] Exception: No write permission for directory: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/CINOEDV/extdata
    
     at #06. getWritablePathname.Arguments(static, ...)
     - getWritablePathname.Arguments() is in environment 'R.utils'
    
     at #05. getWritablePathname(static, ...)
     - getWritablePathname() is in environment 'R.utils'
    
     at #04. Arguments$getWritablePathname(pathname, mustNotExist = FALSE)
     - Arguments$getWritablePathname() is local of the calling function
    
     at #03. writeMat.default(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat.default() is in environment 'R.matlab'
    
     at #02. writeMat(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat() is in environment 'R.matlab'
    
     at #01. BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure,
     Stra, Pop, Iter, SNFName)
     - BatCINOEDV() is in environment 'CINOEDV'
    
    Error: No write permission for directory: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/CINOEDV/extdata
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0
Check: examples
Result: ERROR
    Running examples in ‘CINOEDV-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: BatCINOEDV
    > ### Title: Batch mode for using CINOEDV
    > ### Aliases: BatCINOEDV
    >
    > ### ** Examples
    >
    > File1 <- system.file("extdata","test.mat",package="CINOEDV")
    > File2 <- system.file("extdata","test1.mat",package="CINOEDV")
    > File3 <- system.file("extdata","test1_Name.mat",package="CINOEDV")
    > FileName <- c(File1,File2)
    > SNFName <- c(NA,File3)
    > MaxOrder <- 2
    > RThreshold <- c(1, 1)
    > NThreshold <- c(10, 10)
    > measure <- 1
    > Stra <- 1
    > Pop <- 10
    > Iter <- 10
    > BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure, Stra, Pop, Iter, SNFName)
     The Maximum order : 2
    
     The RatioThreshold : 1 1
    
     The NumberThreshold : 10 10
    
     The input file is : /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CINOEDV/extdata/test.mat
     Samples: 4000
     Cases: 2000
     Controls: 2000
     SNPs: 10
    
     The SNP Name File : NA
    
    #### Search Results ####
    
     Please waiting for the search ...
     Exhaustive Search !
    
     1-order effect computing ...
    elapsed
     0.039
     2-order effect computing ...
    elapsed
     0.445
    #### Normalization ####
    #### SNP Name Notation ####
    #### Collect Vertices and Edges ####
    #### Construct Complete Graph ####
    dev.new(): using pdf(file="Rplots1.pdf")
    #### Plot Top Effects ####
    dev.new(): using pdf(file="Rplots2.pdf")
    #### Degree Analysis ####
    dev.new(): using pdf(file="Rplots3.pdf")
     SNP Degree
     [1,] "5" "4"
     [2,] "4" "3"
     [3,] "7" "3"
     [4,] "10" "3"
     [5,] "8" "2"
     [6,] "1" "2"
     [7,] "6" "2"
     [8,] "3" "1"
     [9,] "2" "0"
    [10,] "9" "0"
    #### Split subgraphs ####
    dev.new(): using pdf(file="Rplots4.pdf")
    [2018-02-24 16:06:48] Exception: No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CINOEDV/extdata
    
     at #06. getWritablePathname.Arguments(static, ...)
     - getWritablePathname.Arguments() is in environment 'R.utils'
    
     at #05. getWritablePathname(static, ...)
     - getWritablePathname() is in environment 'R.utils'
    
     at #04. Arguments$getWritablePathname(pathname, mustNotExist = FALSE)
     - Arguments$getWritablePathname() is local of the calling function
    
     at #03. writeMat.default(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat.default() is in environment 'R.matlab'
    
     at #02. writeMat(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat() is in environment 'R.matlab'
    
     at #01. BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure,
     Stra, Pop, Iter, SNFName)
     - BatCINOEDV() is in environment 'CINOEDV'
    
    Error: No write permission for directory: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CINOEDV/extdata
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.0
Check: examples
Result: ERROR
    Running examples in ‘CINOEDV-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: BatCINOEDV
    > ### Title: Batch mode for using CINOEDV
    > ### Aliases: BatCINOEDV
    >
    > ### ** Examples
    >
    > File1 <- system.file("extdata","test.mat",package="CINOEDV")
    > File2 <- system.file("extdata","test1.mat",package="CINOEDV")
    > File3 <- system.file("extdata","test1_Name.mat",package="CINOEDV")
    > FileName <- c(File1,File2)
    > SNFName <- c(NA,File3)
    > MaxOrder <- 2
    > RThreshold <- c(1, 1)
    > NThreshold <- c(10, 10)
    > measure <- 1
    > Stra <- 1
    > Pop <- 10
    > Iter <- 10
    > BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure, Stra, Pop, Iter, SNFName)
     The Maximum order : 2
    
     The RatioThreshold : 1 1
    
     The NumberThreshold : 10 10
    
     The input file is : /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/CINOEDV/extdata/test.mat
     Samples: 4000
     Cases: 2000
     Controls: 2000
     SNPs: 10
    
     The SNP Name File : NA
    
    #### Search Results ####
    
     Please waiting for the search ...
     Exhaustive Search !
    
     1-order effect computing ...
    elapsed
     0.231
     2-order effect computing ...
    elapsed
     0.496
    #### Normalization ####
    #### SNP Name Notation ####
    #### Collect Vertices and Edges ####
    #### Construct Complete Graph ####
    dev.new(): using pdf(file="Rplots1.pdf")
    #### Plot Top Effects ####
    dev.new(): using pdf(file="Rplots2.pdf")
    #### Degree Analysis ####
    dev.new(): using pdf(file="Rplots3.pdf")
     SNP Degree
     [1,] "5" "4"
     [2,] "4" "3"
     [3,] "7" "3"
     [4,] "10" "3"
     [5,] "8" "2"
     [6,] "1" "2"
     [7,] "6" "2"
     [8,] "3" "1"
     [9,] "2" "0"
    [10,] "9" "0"
    #### Split subgraphs ####
    dev.new(): using pdf(file="Rplots4.pdf")
    [2018-02-23 16:28:46] Exception: No write permission for directory: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/CINOEDV/extdata
    
     at #06. getWritablePathname.Arguments(static, ...)
     - getWritablePathname.Arguments() is in environment 'R.utils'
    
     at #05. getWritablePathname(static, ...)
     - getWritablePathname() is in environment 'R.utils'
    
     at #04. Arguments$getWritablePathname(pathname, mustNotExist = FALSE)
     - Arguments$getWritablePathname() is local of the calling function
    
     at #03. writeMat.default(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat.default() is in environment 'R.matlab'
    
     at #02. writeMat(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat() is in environment 'R.matlab'
    
     at #01. BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure,
     Stra, Pop, Iter, SNFName)
     - BatCINOEDV() is in environment 'CINOEDV'
    
    Error: No write permission for directory: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/CINOEDV/extdata
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 2.0
Check: examples
Result: ERROR
    Running examples in ‘CINOEDV-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: BatCINOEDV
    > ### Title: Batch mode for using CINOEDV
    > ### Aliases: BatCINOEDV
    >
    > ### ** Examples
    >
    > File1 <- system.file("extdata","test.mat",package="CINOEDV")
    > File2 <- system.file("extdata","test1.mat",package="CINOEDV")
    > File3 <- system.file("extdata","test1_Name.mat",package="CINOEDV")
    > FileName <- c(File1,File2)
    > SNFName <- c(NA,File3)
    > MaxOrder <- 2
    > RThreshold <- c(1, 1)
    > NThreshold <- c(10, 10)
    > measure <- 1
    > Stra <- 1
    > Pop <- 10
    > Iter <- 10
    > BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure, Stra, Pop, Iter, SNFName)
     The Maximum order : 2
    
     The RatioThreshold : 1 1
    
     The NumberThreshold : 10 10
    
     The input file is : /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/CINOEDV/extdata/test.mat
     Samples: 4000
     Cases: 2000
     Controls: 2000
     SNPs: 10
    
     The SNP Name File : NA
    
    #### Search Results ####
    
     Please waiting for the search ...
     Exhaustive Search !
    
     1-order effect computing ...
    elapsed
     0.197
     2-order effect computing ...
    elapsed
     0.436
    #### Normalization ####
    #### SNP Name Notation ####
    #### Collect Vertices and Edges ####
    #### Construct Complete Graph ####
    dev.new(): using pdf(file="Rplots1.pdf")
    #### Plot Top Effects ####
    dev.new(): using pdf(file="Rplots2.pdf")
    #### Degree Analysis ####
    dev.new(): using pdf(file="Rplots3.pdf")
     SNP Degree
     [1,] "5" "4"
     [2,] "4" "3"
     [3,] "7" "3"
     [4,] "10" "3"
     [5,] "8" "2"
     [6,] "1" "2"
     [7,] "6" "2"
     [8,] "3" "1"
     [9,] "2" "0"
    [10,] "9" "0"
    #### Split subgraphs ####
    dev.new(): using pdf(file="Rplots4.pdf")
    [2018-02-24 04:27:40] Exception: No write permission for directory: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/CINOEDV/extdata
    
     at #06. getWritablePathname.Arguments(static, ...)
     - getWritablePathname.Arguments() is in environment 'R.utils'
    
     at #05. getWritablePathname(static, ...)
     - getWritablePathname() is in environment 'R.utils'
    
     at #04. Arguments$getWritablePathname(pathname, mustNotExist = FALSE)
     - Arguments$getWritablePathname() is local of the calling function
    
     at #03. writeMat.default(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat.default() is in environment 'R.matlab'
    
     at #02. writeMat(paste(SaveFileName, ".mat", sep = ""), parameters = parameters,
     data = data, results = results, graphs = graphs)
     - writeMat() is in environment 'R.matlab'
    
     at #01. BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure,
     Stra, Pop, Iter, SNFName)
     - BatCINOEDV() is in environment 'CINOEDV'
    
    Error: No write permission for directory: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/CINOEDV/extdata
    Execution halted
Flavor: r-release-linux-x86_64