Last updated on 2024-04-18 06:09:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.9 | 7.81 | 98.14 | 105.95 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.9 | 7.90 | 72.93 | 80.83 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.9 | 133.63 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.9 | 139.86 | OK | |||
| r-prerel-macos-arm64 | 3.9 | 48.00 | OK | |||
| r-prerel-macos-x86_64 | 3.9 | 136.00 | OK | |||
| r-prerel-windows-x86_64 | 3.9 | 10.00 | 99.00 | 109.00 | OK | |
| r-patched-linux-x86_64 | 3.8 | 8.38 | 87.10 | 95.48 | ERROR | |
| r-release-linux-x86_64 | 3.9 | 10.32 | 97.01 | 107.33 | OK | |
| r-release-macos-arm64 | 3.9 | 55.00 | OK | |||
| r-release-macos-x86_64 | 3.9 | 116.00 | OK | |||
| r-release-windows-x86_64 | 3.9 | 10.00 | 113.00 | 123.00 | OK | |
| r-oldrel-macos-arm64 | 3.9 | 49.00 | OK | |||
| r-oldrel-windows-x86_64 | 3.9 | 12.00 | 121.00 | 133.00 | OK |
Version: 3.8
Check: examples
Result: ERROR
Running examples in ‘pedgene-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavor: r-patched-linux-x86_64
Version: 3.8
Check: tests
Result: ERROR
Running ‘test.pedgene.R’ [3s/3s]
Running ‘test.pedgene.expanded.R’ [3s/3s]
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
Flavor: r-patched-linux-x86_64
Version: 3.8
Check: re-building of vignette outputs
Result: 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
Flavor: r-patched-linux-x86_64