- using R Under development (unstable) (2024-03-25 r86189)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘pedgene/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘pedgene’ version ‘3.8’
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘pedgene’ can be installed ... [13s/47s] OK
See the install log for details.
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/16s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/15s] OK
- checking whether the package can be unloaded cleanly ... [4s/14s] OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... [3s/10s] OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [17s/52s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [4s/14s] ERROR
Running examples in ‘pedgene-Ex.R’ failed
The error most likely occurred in:
> ### Name: pedgene
> ### Title: Compute Kernel and Burden Statistics for Pedigree Data (possibly
> ### with unrelated subjects)
> ### Aliases: pedgene pedgene.stats print.pedgene summary.pedgene
> ### Keywords: kinship
>
> ### ** Examples
>
> # example data with the same 10 variants for an autosome and X chromosome
> # pedigree data on 39 subjects including 3 families and unrelateds
> data(example.ped)
> data(example.geno)
> data(example.map)
>
> # gene tests (chroms 1 and X) with male.dose=2
> pg.m2 <- pedgene(example.ped, example.geno, example.map, male.dose=2)
Warning in pedgene(example.ped, example.geno, example.map, male.dose = 2) :
NAs introduced by coercion
Error in if (as.numeric(substring(kin2v, 1, nchar(kin2v) - 2)) < 1.5) { :
missing value where TRUE/FALSE needed
Calls: pedgene
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [8s/27s] ERROR
Running ‘test.pedgene.R’ [4s/13s]
Running ‘test.pedgene.expanded.R’ [4s/13s]
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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [16s/24s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘pedgene.Rnw’ using Sweave
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
Warning in pedgene(ped = example.ped, geno = example.geno, map = example.map) :
NAs introduced by coercion
Error: processing vignette 'pedgene.Rnw' failed with diagnostics:
chunk 4 (label = ccbase)
Error in if (as.numeric(substring(kin2v, 1, nchar(kin2v) - 2)) < 1.5) { :
missing value where TRUE/FALSE needed
--- failed re-building ‘pedgene.Rnw’
SUMMARY: processing the following file failed:
‘pedgene.Rnw’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [9s/33s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 3 ERRORs