Running ‘test.pedgene.R’
  Running ‘test.pedgene.expanded.R’
Running the tests in ‘tests/test.pedgene.R’ failed.
Complete output:
  > ## Purpose: Test script for pedgene package
  > ## Testing a simple 10-variant gene on both the X chrom and autosome
  > ## Authors: Dan Schaid and Jason Sinnwell
  > ## Created: 19-AUG-2013
  > ## Updated: 11/7/2013
  > 
  > ## alternatively:
  > require(kinship2)
  Loading required package: kinship2
  Loading required package: Matrix
  Loading required package: quadprog
  > require(pedgene)
  Loading required package: pedgene
  Loading required package: CompQuadForm
  Loading required package: survey
  Loading required package: grid
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > 
  > data(example.ped)
  > data(example.geno)
  > data(example.map)
  > 
  > 
  > if(0) {
  + ## delete above line to look at pedigrees
  + ## quick look at the 3 pedigrees
  +   pedall <- with(example.ped, pedigree(famid=ped, id=person, dadid=father,
  +                 momid=mother, sex=sex, affected=ifelse(is.na(trait), 0, trait)))
  +   
  +   plot(pedall[1])
  +   plot(pedall[2])
  +   plot(pedall[3])
  + }
  > 
  > 
  > ## simple tests of two genes (10 variants each)
  > ## the genes are same variants, just on chroms 1 and X
  > pg.m2 <- pedgene(example.ped, example.geno, example.map, male.dose=2)
  Error in if (as.numeric(substring(kin2v, 1, nchar(kin2v) - 2)) < 1.5) { : 
    missing value where TRUE/FALSE needed
  Calls: pedgene
  In addition: Warning message:
  In pedgene(example.ped, example.geno, example.map, male.dose = 2) :
    NAs introduced by coercion
  Execution halted
Running the tests in ‘tests/test.pedgene.expanded.R’ failed.
Complete output:
  > 
  > ## Expanded test script for pedgene package
  > devel=FALSE
  > if(devel) {
  +   rfiles <- list.files(path="../R/", pattern="*.R$")
  +   for(f in rfiles) source(paste("../R/",f,sep=""))
  +   dfiles <- list.files(path="../data/", pattern="*.RData$")
  +   for(d in dfiles) load(paste("../data/",d,sep=""))
  +   library(kinship2)
  +   library(survey)
  + } else {
  +   
  +   require(pedgene)
  +   data(example.ped)
  +   data(example.geno)
  +   data(example.map)
  +   data(example.relation)
  + }
  Loading required package: pedgene
  Loading required package: Matrix
  Loading required package: CompQuadForm
  Loading required package: survey
  Loading required package: grid
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  Loading required package: kinship2
  Loading required package: quadprog
  > 
  > #require(survery)
  > 
  > 
  > ######################################
  > ## From Dan Weeks, issues to check
  > ######################################
  > ## 1) missid ="0" when the rest of the ids are character
  > ## 2) skip pedigree checking, checkpeds=TRUE/FALSE
  > ## 3) character alleles
  > ## 4) disconnected pedigrees
  > ## 5) "flipped" 0/2 geno counts
  > 
  > ## base case, m-b weights
  > pg.out.m2 <- pedgene(ped=example.ped, geno=example.geno, map=example.map, male.dose=2,
  +                      weights.mb=TRUE,checkpeds=TRUE)
  Error in if (as.numeric(substring(kin2v, 1, nchar(kin2v) - 2)) < 1.5) { : 
    missing value where TRUE/FALSE needed
  Calls: pedgene
  In addition: Warning message:
  In pedgene(ped = example.ped, geno = example.geno, map = example.map,  :
    NAs introduced by coercion
  Execution halted