CRAN Package Check Results for Package pheno2geno

Last updated on 2020-01-27 00:48:11 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4.0 14.84 99.72 114.56 ERROR
r-devel-linux-x86_64-debian-gcc 1.4.0 11.38 87.82 99.20 NOTE
r-devel-linux-x86_64-fedora-clang 1.4.0 152.96 NOTE
r-devel-linux-x86_64-fedora-gcc 1.4.0 149.18 NOTE
r-devel-windows-ix86+x86_64 1.4.0 33.00 164.00 197.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.4.0 35.00 171.00 206.00 OK
r-patched-linux-x86_64 1.4.0 12.14 100.93 113.07 OK
r-patched-solaris-x86 1.4.0 196.20 OK
r-release-linux-x86_64 1.4.0 12.63 100.69 113.32 OK
r-release-windows-ix86+x86_64 1.4.0 20.00 121.00 141.00 OK
r-release-osx-x86_64 1.4.0 NOTE
r-oldrel-windows-ix86+x86_64 1.4.0 13.00 150.00 163.00 OK
r-oldrel-osx-x86_64 1.4.0 OK

Check Details

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: 0x637e998>
    <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' [5s/6s]
    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 1.1.0, Released 2017-03-10
     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: 0xcaff290>
     <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: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘mycross.csv’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, 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