Last updated on 2020-02-19 10:49:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.0 | 14.92 | 120.69 | 135.61 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.4.0 | 12.43 | 93.66 | 106.09 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.4.0 | 165.03 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.0 | 161.09 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.4.0 | 24.00 | 138.00 | 162.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.4.0 | 38.00 | 155.00 | 193.00 | OK | |
| r-patched-linux-x86_64 | 1.4.0 | 13.04 | 115.03 | 128.07 | OK | |
| r-patched-solaris-x86 | 1.4.0 | 228.00 | OK | |||
| r-release-linux-x86_64 | 1.4.0 | 15.62 | 115.26 | 130.88 | OK | |
| r-release-windows-ix86+x86_64 | 1.4.0 | 23.00 | 126.00 | 149.00 | OK | |
| r-release-osx-x86_64 | 1.4.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.4.0 | 14.00 | 123.00 | 137.00 | OK | |
| r-oldrel-osx-x86_64 | 1.4.0 | OK |
Version: 1.4.0
Check: examples
Result: ERROR
Running examples in 'pheno2geno-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add.to.population
> ### Title: Add additional data to a population object
> ### Aliases: add.to.population add.to.populationSub.internal dataObject
> ### dataType
> ### Keywords: manip
>
> ### ** Examples
>
> population <- fake.population()
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject)
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(pheno, founders, foundersGroups, geno, map,
physicalMap, verbose = verbose)
where 3: fake.population()
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0xd347308>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject) :
the condition has length > 1
Calls: fake.population -> create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.4.0
Check: tests
Result: ERROR
Running 'test_analysis.R' [6s/8s]
Running the tests in 'tests/test_analysis.R' failed.
Complete output:
> require(pheno2geno)
Loading required package: pheno2geno
Loading required package: qtl
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: mixtools
mixtools package, version 1.2.0, Released 2020-02-05
This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
> #setwd("C:/Users/Konrad/Documents/Github/phenotypes2genotypes/tests")
> children <- read.csv(file="offspring_phenotypes.csv",header=TRUE,row.names=1)
> parents <- read.csv(file="parental_phenotypes.csv",header=TRUE,row.names=1)
> genotypes <- read.csv(file="genotypes.csv",header=TRUE,row.names=1)
> map <- read.csv(file="map.csv",header=TRUE,row.names=1)
>
> #with parental data
> population <- create.population(children,parents,c(0,0,0,0,0,0,1,1,1,1,1,1),genotypes,mapsPhysical=map,verbose=TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame")
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(children, parents, c(0, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1, 1), genotypes, mapsPhysical = map, verbose = TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0x9af02c8>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame") :
the condition has length > 1
Calls: create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.4.0
Check: examples
Result: ERROR
Running examples in ‘pheno2geno-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add.to.population
> ### Title: Add additional data to a population object
> ### Aliases: add.to.population add.to.populationSub.internal dataObject
> ### dataType
> ### Keywords: manip
>
> ### ** Examples
>
> population <- fake.population()
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject)
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(pheno, founders, foundersGroups, geno, map,
physicalMap, verbose = verbose)
where 3: fake.population()
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0x56435df89838>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject) :
the condition has length > 1
Calls: fake.population -> create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.0
Check: tests
Result: ERROR
Running ‘test_analysis.R’ [5s/7s]
Running the tests in ‘tests/test_analysis.R’ failed.
Complete output:
> require(pheno2geno)
Loading required package: pheno2geno
Loading required package: qtl
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: mixtools
mixtools package, version 1.2.0, Released 2020-02-05
This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
> #setwd("C:/Users/Konrad/Documents/Github/phenotypes2genotypes/tests")
> children <- read.csv(file="offspring_phenotypes.csv",header=TRUE,row.names=1)
> parents <- read.csv(file="parental_phenotypes.csv",header=TRUE,row.names=1)
> genotypes <- read.csv(file="genotypes.csv",header=TRUE,row.names=1)
> map <- read.csv(file="map.csv",header=TRUE,row.names=1)
>
> #with parental data
> population <- create.population(children,parents,c(0,0,0,0,0,0,1,1,1,1,1,1),genotypes,mapsPhysical=map,verbose=TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame")
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(children, parents, c(0, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1, 1), genotypes, mapsPhysical = map, verbose = TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0x55779d3a7c88>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame") :
the condition has length > 1
Calls: create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4.0
Check: examples
Result: ERROR
Running examples in ‘pheno2geno-Ex.R’ failed
The error most likely occurred in:
> ### Name: add.to.population
> ### Title: Add additional data to a population object
> ### Aliases: add.to.population add.to.populationSub.internal dataObject
> ### dataType
> ### Keywords: manip
>
> ### ** Examples
>
> population <- fake.population()
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject)
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(pheno, founders, foundersGroups, geno, map,
physicalMap, verbose = verbose)
where 3: fake.population()
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0xae54b00>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject) :
the condition has length > 1
Calls: fake.population -> create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.4.0
Check: tests
Result: ERROR
Running ‘test_analysis.R’
Running the tests in ‘tests/test_analysis.R’ failed.
Complete output:
> require(pheno2geno)
Loading required package: pheno2geno
Loading required package: qtl
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: mixtools
mixtools package, version 1.2.0, Released 2020-02-05
This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
> #setwd("C:/Users/Konrad/Documents/Github/phenotypes2genotypes/tests")
> children <- read.csv(file="offspring_phenotypes.csv",header=TRUE,row.names=1)
> parents <- read.csv(file="parental_phenotypes.csv",header=TRUE,row.names=1)
> genotypes <- read.csv(file="genotypes.csv",header=TRUE,row.names=1)
> map <- read.csv(file="map.csv",header=TRUE,row.names=1)
>
> #with parental data
> population <- create.population(children,parents,c(0,0,0,0,0,0,1,1,1,1,1,1),genotypes,mapsPhysical=map,verbose=TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame")
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(children, parents, c(0, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1, 1), genotypes, mapsPhysical = map, verbose = TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0x7550da8>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame") :
the condition has length > 1
Calls: create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.4.0
Check: examples
Result: ERROR
Running examples in ‘pheno2geno-Ex.R’ failed
The error most likely occurred in:
> ### Name: add.to.population
> ### Title: Add additional data to a population object
> ### Aliases: add.to.population add.to.populationSub.internal dataObject
> ### dataType
> ### Keywords: manip
>
> ### ** Examples
>
> population <- fake.population()
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject)
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(pheno, founders, foundersGroups, geno, map,
physicalMap, verbose = verbose)
where 3: fake.population()
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0xda10bc8>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) == "data.frame") dataObject <- as.matrix(dataObject) :
the condition has length > 1
Calls: fake.population -> create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.4.0
Check: tests
Result: ERROR
Running ‘test_analysis.R’
Running the tests in ‘tests/test_analysis.R’ failed.
Complete output:
> require(pheno2geno)
Loading required package: pheno2geno
Loading required package: qtl
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: mixtools
mixtools package, version 1.2.0, Released 2020-02-05
This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
> #setwd("C:/Users/Konrad/Documents/Github/phenotypes2genotypes/tests")
> children <- read.csv(file="offspring_phenotypes.csv",header=TRUE,row.names=1)
> parents <- read.csv(file="parental_phenotypes.csv",header=TRUE,row.names=1)
> genotypes <- read.csv(file="genotypes.csv",header=TRUE,row.names=1)
> map <- read.csv(file="map.csv",header=TRUE,row.names=1)
>
> #with parental data
> population <- create.population(children,parents,c(0,0,0,0,0,0,1,1,1,1,1,1),genotypes,mapsPhysical=map,verbose=TRUE)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
pheno2geno
--- call from context ---
add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
--- call from argument ---
if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame")
--- R stacktrace ---
where 1: add.to.populationSub.internal(population, populationType, offspringPhenotypes,
"offspring$phenotypes", verbose, debugMode)
where 2: create.population(children, parents, c(0, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1, 1), genotypes, mapsPhysical = map, verbose = TRUE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (population, populationType = c("riself", "f2", "bc",
"risib"), dataObject, dataType = c("founders", "offspring$phenotypes",
"founders$groups", "offspring$genotypes", "maps$genetic",
"maps$physical", "annotations"), verbose = FALSE, debugMode = 0)
{
dataType <- match.arg(dataType)
populationType <- match.arg(populationType)
if (missing(dataObject))
stop("dataObject is missing\n")
if (dataType != "founders$groups") {
if (class(dataObject) == "data.frame")
dataObject <- as.matrix(dataObject)
if (class(dataObject) != "matrix")
stop("dataObject should be either a matrix or a date frame")
}
if (dataType == "founders" || dataType == "offspring$phenotypes") {
population <- add.to.populationSubPheno.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "offspring$genotypes") {
if (!(is.null(dataObject)) && !is.null(dim(dataObject))) {
population$offspring$genotypes$real <- add.to.populationSubGeno.internal(population,
dataObject, populationType, verbose)
}
else {
stop("No data provided for offspring$genotypes !\n")
}
}
else if (dataType == "maps$genetic" || dataType == "maps$physical") {
population <- add.to.populationSubMap.internal(population,
dataObject, dataType, verbose, debugMode)
}
else if (dataType == "founders$groups") {
population$founders$groups <- dataObject
}
else {
population <- add.to.populationSubAnnots.internal(population,
dataObject, verbose, debugMode)
}
invisible(population)
}
<bytecode: 0x9594a30>
<environment: namespace:pheno2geno>
--- function search by body ---
Function add.to.populationSub.internal in namespace pheno2geno has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(dataObject) != "matrix") stop("dataObject should be either a matrix or a date frame") :
the condition has length > 1
Calls: create.population -> add.to.populationSub.internal
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.4.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘RankProd’
Flavor: r-release-osx-x86_64
Version: 1.4.0
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘RankProd’
Flavor: r-release-osx-x86_64