Last updated on 2019-12-16 10:48:24 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.6 | 3.61 | 24.88 | 28.49 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 4.6 | 2.86 | 20.87 | 23.73 | OK | |
| r-devel-linux-x86_64-fedora-clang | 4.6 | 37.25 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 4.6 | 37.05 | OK | |||
| r-devel-windows-ix86+x86_64 | 4.6 | 8.00 | 54.00 | 62.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 4.6 | 6.00 | 51.00 | 57.00 | OK | |
| r-patched-linux-x86_64 | 4.6 | 2.86 | 24.56 | 27.42 | OK | |
| r-patched-solaris-x86 | 4.6 | 51.70 | OK | |||
| r-release-linux-x86_64 | 4.6 | 2.93 | 24.36 | 27.29 | OK | |
| r-release-windows-ix86+x86_64 | 4.6 | 6.00 | 49.00 | 55.00 | OK | |
| r-release-osx-x86_64 | 4.6 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 4.6 | 3.00 | 32.00 | 35.00 | OK | |
| r-oldrel-osx-x86_64 | 4.6 | OK |
Version: 4.6
Check: examples
Result: ERROR
Running examples in 'rrBLUP-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GWAS
> ### Title: Genome-wide association analysis
> ### Aliases: GWAS
>
> ### ** Examples
>
> #random population of 200 lines with 1000 markers
> M <- matrix(rep(0,200*1000),1000,200)
> for (i in 1:200) {
+ M[,i] <- ifelse(runif(1000)<0.5,-1,1)
+ }
> colnames(M) <- 1:200
> geno <- data.frame(marker=1:1000,chrom=rep(1,1000),pos=1:1000,M,check.names=FALSE)
>
> QTL <- 100*(1:5) #pick 5 QTL
> u <- rep(0,1000) #marker effects
> u[QTL] <- 1
> g <- as.vector(crossprod(M,u))
> h2 <- 0.5
> y <- g + rnorm(200,mean=0,sd=sqrt((1-h2)/h2*var(g)))
>
> pheno <- data.frame(line=1:200,y=y)
> scores <- GWAS(pheno,geno,plot=FALSE)
[1] "GWAS for trait: y"
[1] "Variance components estimated. Testing markers."
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
rrBLUP
--- call from context ---
score.calc(M[ix.pheno, ])
--- call from argument ---
if (class(Winv) != "try-error") {
beta <- Winv %*% crossprod(X3, H2inv %*% y2)
resid <- y2 - X3 %*% beta
s2 <- as.double(crossprod(resid, H2inv %*% resid))/v2
CovBeta <- s2 * Winv
Fstat <- beta[p]^2/CovBeta[p, p]
x <- v2/(v2 + v1 * Fstat)
scores[i] <- -log10(pbeta(x, v2/2, v1/2))
}
--- R stacktrace ---
where 1: score.calc(M[ix.pheno, ])
where 2: GWAS(pheno, geno, plot = FALSE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (M)
{
m <- ncol(M)
scores <- array(0, m)
for (i in 1:m) {
Mi <- M[, i]
freq <- mean(Mi + 1, na.rm = TRUE)/2
MAF <- min(freq, 1 - freq)
if (MAF >= min.MAF) {
not.NA.gid <- which(!is.na(Mi))
temp <- rep(1, length(Mi))
temp[not.NA.gid] <- 0
not.NA.obs <- which(Z %*% temp != 1)
n2 <- length(not.NA.obs)
y2 <- matrix(y[not.NA.obs], n2, 1)
Z2 <- Z[not.NA.obs, not.NA.gid]
X3 <- cbind(X2[not.NA.obs, ], Z2 %*% Mi[not.NA.gid])
p <- ncol(X3)
v1 <- 1
v2 <- n2 - p
if (!P3D) {
H2inv <- mixed.solve(y = y2, X = X3, Z = Z2,
K = K2[not.NA.gid, not.NA.gid], return.Hinv = TRUE)$Hinv
}
else {
H2inv <- Hinv[not.NA.obs, not.NA.obs]
}
W <- crossprod(X3, H2inv %*% X3)
Winv <- try(solve(W), silent = TRUE)
if (class(Winv) != "try-error") {
beta <- Winv %*% crossprod(X3, H2inv %*% y2)
resid <- y2 - X3 %*% beta
s2 <- as.double(crossprod(resid, H2inv %*% resid))/v2
CovBeta <- s2 * Winv
Fstat <- beta[p]^2/CovBeta[p, p]
x <- v2/(v2 + v1 * Fstat)
scores[i] <- -log10(pbeta(x, v2/2, v1/2))
}
}
}
return(scores)
}
<bytecode: 0x28eae90>
<environment: 0x28e2a90>
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Error in if (class(Winv) != "try-error") { : the condition has length > 1
Calls: GWAS -> score.calc
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang