CRAN Package Check Results for Package MOJOV

Last updated on 2020-02-15 01:01:30 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 9.91 72.05 81.96 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.1 9.13 57.22 66.35 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.1 101.37 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.1 101.81 ERROR
r-devel-windows-ix86+x86_64 1.0.1 23.00 87.00 110.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 1.0.1 28.00 110.00 138.00 NOTE
r-patched-linux-x86_64 1.0.1 8.14 64.22 72.36 NOTE
r-patched-solaris-x86 1.0.1 135.10 NOTE
r-release-linux-x86_64 1.0.1 8.96 63.94 72.90 NOTE
r-release-windows-ix86+x86_64 1.0.1 17.00 79.00 96.00 NOTE
r-release-osx-x86_64 1.0.1 NOTE
r-oldrel-windows-ix86+x86_64 1.0.1 13.00 72.00 85.00 NOTE
r-oldrel-osx-x86_64 1.0.1 NOTE

Check Details

Version: 1.0.1
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: 'methods'
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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-devel-windows-ix86+x86_64-gcc8, 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: 1.0.1
Check: R code for possible problems
Result: NOTE
    MOJOV.analysis: no visible global function definition for 'lm'
    MOJOV.analysis: no visible global function definition for 'read.csv'
    MOJOV.analysis: no visible global function definition for
     'txtProgressBar'
    MOJOV.analysis: no visible global function definition for
     'setTxtProgressBar'
    MOJOV.analysis: no visible global function definition for 'write.csv'
    MOJOV.analysis: no visible global function definition for 'new'
    MOJOV.export: no visible global function definition for 'write.table'
    MOJOV.linearRegAnalysis: no visible global function definition for 'lm'
    MOJOV.phenotype: no visible global function definition for
     'shapiro.test'
    MOJOV.phenotype: no visible global function definition for 'glm'
    MOJOV.phenotype: no visible global function definition for 'new'
    MOJOV.read: no visible global function definition for 'read.csv'
    MOJOV.read: no visible global function definition for 'new'
    MOJOV.regTermTest: no visible global function definition for 'glm'
    MOJOV.saws: no visible global function definition for 'model.matrix'
    MOJOV.saws: no visible global function definition for 'glm'
    MOJOV.simulation: no visible global function definition for
     'txtProgressBar'
    MOJOV.simulation : <anonymous>: no visible global function definition
     for 'rnorm'
    MOJOV.simulation: no visible global function definition for 'rnorm'
    MOJOV.simulation: no visible global function definition for
     'setTxtProgressBar'
    MOJOV.simulation: no visible global function definition for 'write.csv'
    MOJOV.summary: no visible global function definition for
     'txtProgressBar'
    MOJOV.summary: no visible global function definition for
     'setTxtProgressBar'
    MOJOV.summary: no visible global function definition for 'new'
    MOJOV.wald.test: no visible global function definition for 'glm'
    MOJOV.weight: no visible global function definition for 'sd'
    Undefined global functions or variables:
     glm lm model.matrix new read.csv rnorm sd setTxtProgressBar
     shapiro.test txtProgressBar write.csv write.table
    Consider adding
     importFrom("methods", "new")
     importFrom("stats", "glm", "lm", "model.matrix", "rnorm", "sd",
     "shapiro.test")
     importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar",
     "write.csv", "write.table")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
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-devel-windows-ix86+x86_64-gcc8, 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: 1.0.1
Check: examples
Result: ERROR
    Running examples in 'MOJOV-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: MOJOV.analysis
    > ### Title: Analysis between rare variants and quantatitive traits using
    > ### CMC.
    > ### Aliases: MOJOV.analysis
    >
    > ### ** Examples
    >
    > file1<-system.file("data","geno.csv.gz",package="MOJOV")
    > file2<-system.file("data","phen.csv.gz",package="MOJOV")
    > x<-MOJOV.read(genofile=file1,phenofile=file2)
    > x<-MOJOV.phenotype(x=x)
    > x<-MOJOV.analysis(x=x)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    MOJOV
     --- call from context ---
    MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
     --- call from argument ---
    if (class(x) != "matrix") stop("The data x should be a matrix.")
     --- R stacktrace ---
    where 1: MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
    where 2: MOJOV.analysis(x = x)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (x = NULL, y = NULL, codeMethod = c("Proportion", "Indicator",
     "ChuanhuaXin"), weightMethod = c("ChuanhuaXin"))
    {
     if (is.null(x) | is.null(y))
     stop("You need specify your data.")
     if (class(x) != "matrix")
     stop("The data x should be a matrix.")
     if (length(y) != dim(x)[1])
     stop("The genotype matrix x is not conformable.")
     codeMethod <- match.arg(codeMethod)
     if (codeMethod == "ChuanhuaXin") {
     weight <- MOJOV.weight(x = x, y = y, weightMethod = weightMethod)
     X <- apply(x, 1, function(x) sum(x * weight))
     }
     if (codeMethod == "Proportion") {
     X <- apply(x, 1, sum)/(dim(x)[2] * 2)
     }
     if (codeMethod == "Indicator") {
     X <- apply(x, 1, sum)
     X <- unlist(lapply(X, function(x) ifelse(x > 0, 1, 0)))
     }
     return(X)
    }
    <bytecode: 0x969bfe0>
    <environment: namespace:MOJOV>
     --- function search by body ---
    Function MOJOV.genoVector in namespace MOJOV has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x) != "matrix") stop("The data x should be a matrix.") :
     the condition has length > 1
    Calls: MOJOV.analysis -> MOJOV.genoVector
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘MOJOV-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: MOJOV.analysis
    > ### Title: Analysis between rare variants and quantatitive traits using
    > ### CMC.
    > ### Aliases: MOJOV.analysis
    >
    > ### ** Examples
    >
    > file1<-system.file("data","geno.csv.gz",package="MOJOV")
    > file2<-system.file("data","phen.csv.gz",package="MOJOV")
    > x<-MOJOV.read(genofile=file1,phenofile=file2)
    > x<-MOJOV.phenotype(x=x)
    > x<-MOJOV.analysis(x=x)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    MOJOV
     --- call from context ---
    MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
     --- call from argument ---
    if (class(x) != "matrix") stop("The data x should be a matrix.")
     --- R stacktrace ---
    where 1: MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
    where 2: MOJOV.analysis(x = x)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (x = NULL, y = NULL, codeMethod = c("Proportion", "Indicator",
     "ChuanhuaXin"), weightMethod = c("ChuanhuaXin"))
    {
     if (is.null(x) | is.null(y))
     stop("You need specify your data.")
     if (class(x) != "matrix")
     stop("The data x should be a matrix.")
     if (length(y) != dim(x)[1])
     stop("The genotype matrix x is not conformable.")
     codeMethod <- match.arg(codeMethod)
     if (codeMethod == "ChuanhuaXin") {
     weight <- MOJOV.weight(x = x, y = y, weightMethod = weightMethod)
     X <- apply(x, 1, function(x) sum(x * weight))
     }
     if (codeMethod == "Proportion") {
     X <- apply(x, 1, sum)/(dim(x)[2] * 2)
     }
     if (codeMethod == "Indicator") {
     X <- apply(x, 1, sum)
     X <- unlist(lapply(X, function(x) ifelse(x > 0, 1, 0)))
     }
     return(X)
    }
    <bytecode: 0x55e2a34d47d0>
    <environment: namespace:MOJOV>
     --- function search by body ---
    Function MOJOV.genoVector in namespace MOJOV has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x) != "matrix") stop("The data x should be a matrix.") :
     the condition has length > 1
    Calls: MOJOV.analysis -> MOJOV.genoVector
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘MOJOV-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: MOJOV.analysis
    > ### Title: Analysis between rare variants and quantatitive traits using
    > ### CMC.
    > ### Aliases: MOJOV.analysis
    >
    > ### ** Examples
    >
    > file1<-system.file("data","geno.csv.gz",package="MOJOV")
    > file2<-system.file("data","phen.csv.gz",package="MOJOV")
    > x<-MOJOV.read(genofile=file1,phenofile=file2)
    > x<-MOJOV.phenotype(x=x)
    > x<-MOJOV.analysis(x=x)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    MOJOV
     --- call from context ---
    MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
     --- call from argument ---
    if (class(x) != "matrix") stop("The data x should be a matrix.")
     --- R stacktrace ---
    where 1: MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
    where 2: MOJOV.analysis(x = x)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (x = NULL, y = NULL, codeMethod = c("Proportion", "Indicator",
     "ChuanhuaXin"), weightMethod = c("ChuanhuaXin"))
    {
     if (is.null(x) | is.null(y))
     stop("You need specify your data.")
     if (class(x) != "matrix")
     stop("The data x should be a matrix.")
     if (length(y) != dim(x)[1])
     stop("The genotype matrix x is not conformable.")
     codeMethod <- match.arg(codeMethod)
     if (codeMethod == "ChuanhuaXin") {
     weight <- MOJOV.weight(x = x, y = y, weightMethod = weightMethod)
     X <- apply(x, 1, function(x) sum(x * weight))
     }
     if (codeMethod == "Proportion") {
     X <- apply(x, 1, sum)/(dim(x)[2] * 2)
     }
     if (codeMethod == "Indicator") {
     X <- apply(x, 1, sum)
     X <- unlist(lapply(X, function(x) ifelse(x > 0, 1, 0)))
     }
     return(X)
    }
    <bytecode: 0x8d37520>
    <environment: namespace:MOJOV>
     --- function search by body ---
    Function MOJOV.genoVector in namespace MOJOV has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x) != "matrix") stop("The data x should be a matrix.") :
     the condition has length > 1
    Calls: MOJOV.analysis -> MOJOV.genoVector
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘MOJOV-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: MOJOV.analysis
    > ### Title: Analysis between rare variants and quantatitive traits using
    > ### CMC.
    > ### Aliases: MOJOV.analysis
    >
    > ### ** Examples
    >
    > file1<-system.file("data","geno.csv.gz",package="MOJOV")
    > file2<-system.file("data","phen.csv.gz",package="MOJOV")
    > x<-MOJOV.read(genofile=file1,phenofile=file2)
    > x<-MOJOV.phenotype(x=x)
    > x<-MOJOV.analysis(x=x)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    MOJOV
     --- call from context ---
    MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
     --- call from argument ---
    if (class(x) != "matrix") stop("The data x should be a matrix.")
     --- R stacktrace ---
    where 1: MOJOV.genoVector(x = tmp, y = adjustData, codeMethod = codeMethod,
     weightMethod = weightMethod, ...)
    where 2: MOJOV.analysis(x = x)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (x = NULL, y = NULL, codeMethod = c("Proportion", "Indicator",
     "ChuanhuaXin"), weightMethod = c("ChuanhuaXin"))
    {
     if (is.null(x) | is.null(y))
     stop("You need specify your data.")
     if (class(x) != "matrix")
     stop("The data x should be a matrix.")
     if (length(y) != dim(x)[1])
     stop("The genotype matrix x is not conformable.")
     codeMethod <- match.arg(codeMethod)
     if (codeMethod == "ChuanhuaXin") {
     weight <- MOJOV.weight(x = x, y = y, weightMethod = weightMethod)
     X <- apply(x, 1, function(x) sum(x * weight))
     }
     if (codeMethod == "Proportion") {
     X <- apply(x, 1, sum)/(dim(x)[2] * 2)
     }
     if (codeMethod == "Indicator") {
     X <- apply(x, 1, sum)
     X <- unlist(lapply(X, function(x) ifelse(x > 0, 1, 0)))
     }
     return(X)
    }
    <bytecode: 0x7f46fe8>
    <environment: namespace:MOJOV>
     --- function search by body ---
    Function MOJOV.genoVector in namespace MOJOV has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(x) != "matrix") stop("The data x should be a matrix.") :
     the condition has length > 1
    Calls: MOJOV.analysis -> MOJOV.genoVector
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc