Last updated on 2020-02-19 10:49:00 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 10.38 | 74.68 | 85.06 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 8.90 | 58.41 | 67.31 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 102.48 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 101.64 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.1 | 16.00 | 74.00 | 90.00 | 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 | 9.34 | 64.26 | 73.60 | NOTE | |
| r-patched-solaris-x86 | 1.0.1 | 135.10 | NOTE | |||
| r-release-linux-x86_64 | 1.0.1 | 8.38 | 64.06 | 72.44 | 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 | 12.00 | 81.00 | 93.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.0.1 | NOTE |
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: 0x5f05e50>
<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: 0x55e0d367e910>
<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: 0x6c33108>
<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: 0x7347948>
<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