CRAN Package Check Results for Package rrBLUP

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

Check Details

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