Last updated on 2025-06-20 09:51:26 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5 | 23.15 | 37.88 | 61.03 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.5 | 19.36 | 29.59 | 48.95 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.5 | 113.89 | ERROR | |||
| r-devel-windows-x86_64 | 0.5 | 31.00 | 73.00 | 104.00 | OK | |
| r-patched-linux-x86_64 | 0.5 | 24.92 | 35.75 | 60.67 | OK | |
| r-release-linux-x86_64 | 0.5 | 26.92 | 35.69 | 62.61 | OK | |
| r-release-macos-arm64 | 0.5 | 58.00 | OK | |||
| r-release-macos-x86_64 | 0.5 | 96.00 | OK | |||
| r-release-windows-x86_64 | 0.5 | 31.00 | 76.00 | 107.00 | OK | |
| r-oldrel-macos-arm64 | 0.5 | 52.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.5 | 86.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.5 | 37.00 | 86.00 | 123.00 | NOTE |
Version: 0.5
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Jiehuan Sun <jiehuan.sun@yale.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Jiehuan",
family = "Sun",
role = c("aut", "cre"),
email = "jiehuan.sun@yale.edu"),
person(given = c("Joshua", "L."),
family = "Warren",
role = "aut"),
person(given = "Hongyu",
family = "Zhao",
role = "aut"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.5
Check: examples
Result: ERROR
Running examples in ‘BCSub-Ex.R’ failed
The error most likely occurred in:
> ### Name: BCSub
> ### Title: A Bayesian semiparametric factor analysis model for subtype
> ### identification (Clustering).
> ### Aliases: BCSub
>
> ### ** Examples
>
> set.seed(1)
> n = 100 ## number of subjects
> G = 200 ## number of genes
> SNR = 0 ## ratio of noise genes
> ## loading matrix with four factors
> lam = matrix(0,G,4)
> lam[1:(G/4),1] = runif(G/4,-3,3)
> lam[(G/4+1):(G/2),2] = runif(G/4,-3,3)
> lam[(G/2+1):(3*G/4),3] = runif(G/4,-3,3)
> lam[(3*G/4+1):(G),4] = runif(G/4,-3,3)
> ## generate low-rank covariance matrix
> sigma <- lam%*%t(lam) + diag(rep(1,G))
> sigma <- cov2cor(sigma)
> ## true cluster structure ##
> e.true = c(rep(1,n/2),rep(2,n/2))
>
> ## generate data matrix ##
> mu1 = rep(1,G)
> mu1[sample(1:G,SNR*G)] = 0
> mu2 <- rep(0,G)
> A = rbind(mvrnorm(n/2,mu1,sigma),mvrnorm(n/2,mu2,sigma))
>
> ## factor analysis to decide the number of factors
> ## Not run:
> ##D ev = eigen(cor(A))
> ##D ap = parallel(subject=nrow(A),var=ncol(A),rep=100,cent=.05)
> ##D nS = nScree(x=ev$values, aparallel=ap$eigen$qevpea)
> ##D M = nS$Components[1,3] ## number of factors
> ## End(Not run)
> M = 4
> ## run BCSub for clustering
> iters = 1000 ## total number of iterations
> seq = 600:1000 ## posterior samples used for inference
> system.time(res <- BCSub(A,iter=iters,seq=seq,M=M))
user system elapsed
12.677 0.301 34.193
> res$CL ## inferred cluster structure
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[38] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[75] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
>
> ## calculate and plot similarity matrix
> sim = calSim(t(res$E[,seq]))
>
> ## plot similarity matrix
> x <- rep(1:n,times=n)
> y <- rep(1:n,each=n)
> z <- as.vector(sim)
> levelplot(z~x*y,col.regions=rev(gray.colors(n^2)), xlab = "Subject ID",ylab = "Subject ID")
Error in levelplot(z ~ x * y, col.regions = rev(gray.colors(n^2)), xlab = "Subject ID", :
could not find function "levelplot"
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64