Last updated on 2019-06-18 01:48:38 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 84.67 | 66.55 | 151.22 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 64.78 | 52.68 | 117.46 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 227.84 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 196.20 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.0.3 | 237.00 | 189.00 | 426.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.3 | 77.30 | 66.38 | 143.68 | NOTE | |
| r-patched-solaris-x86 | 1.0.3 | 220.90 | OK | |||
| r-release-linux-x86_64 | 1.0.3 | 75.69 | 68.30 | 143.99 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.0.3 | 188.00 | 199.00 | 387.00 | ERROR | |
| r-release-osx-x86_64 | 1.0.3 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.3 | 166.00 | 192.00 | 358.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.3 | NOTE |
Version: 1.0.3
Check: use of SHLIB_OPENMP_*FLAGS in Makefiles
Result: NOTE
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
Extensions'. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.3
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'snplistdb.sqlite'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.3
Check: installed package size
Result: NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
libs 8.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-oldrel-osx-x86_64
Version: 1.0.3
Check: running examples for arch ‘i386’
Result: ERROR
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:
> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
>
> ### ** Examples
>
> # Generate dummy data
> set.seed(111)
> n <- 24
>
> # effect size
> beta <- 0.3
>
> # covariate parameters
> theta <- c(0.2, 0.2)
>
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
>
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z <- matrix(cbind(z1, z2), ncol = 2)
>
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
>
> # number of observation times
> ntps <- 5
>
> # number of intervals
> r <- ntps + 1
>
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
>
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
>
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
>
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
>
> # compute efficient score statistics
> res <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta)
> res
[,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,] 0.09537326
[6,] 0.50679716
[7,] -0.01163486
[8,] -0.02150784
>
>
>
> cleanEx()
Error: connections left open:
<-CRANwin.fb05.statistik.uni-dortmund.de:11473 (sockconn)
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 1.0.3
Check: running examples for arch ‘x64’
Result: ERROR
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:
> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
>
> ### ** Examples
>
> # Generate dummy data
> set.seed(111)
> n <- 24
>
> # effect size
> beta <- 0.3
>
> # covariate parameters
> theta <- c(0.2, 0.2)
>
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
>
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z <- matrix(cbind(z1, z2), ncol = 2)
>
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
>
> # number of observation times
> ntps <- 5
>
> # number of intervals
> r <- ntps + 1
>
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
>
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
>
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
>
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
>
> # compute efficient score statistics
> res <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta)
> res
[,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,] 0.09537326
[6,] 0.50679716
[7,] -0.01163486
[8,] -0.02150784
>
>
>
> cleanEx()
Error: connections left open:
<-CRANwin.fb05.statistik.uni-dortmund.de:11274 (sockconn)
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 1.0.3
Check: running examples for arch ‘i386’
Result: ERROR
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:
> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
>
> ### ** Examples
>
> # Generate dummy data
> set.seed(111)
> n <- 24
>
> # effect size
> beta <- 0.3
>
> # covariate parameters
> theta <- c(0.2, 0.2)
>
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
>
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z <- matrix(cbind(z1, z2), ncol = 2)
>
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
>
> # number of observation times
> ntps <- 5
>
> # number of intervals
> r <- ntps + 1
>
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
>
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
>
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
>
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
>
> # compute efficient score statistics
> res <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta)
> res
[,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,] 0.09537326
[6,] 0.50679716
[7,] -0.01163486
[8,] -0.02150784
>
>
>
> cleanEx()
Error: connections left open:
<-CRANwin.fb05.statistik.uni-dortmund.de:11025 (sockconn)
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 1.0.3
Check: running examples for arch ‘x64’
Result: ERROR
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:
> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
>
> ### ** Examples
>
> # Generate dummy data
> set.seed(111)
> n <- 24
>
> # effect size
> beta <- 0.3
>
> # covariate parameters
> theta <- c(0.2, 0.2)
>
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
>
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z <- matrix(cbind(z1, z2), ncol = 2)
>
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
>
> # number of observation times
> ntps <- 5
>
> # number of intervals
> r <- ntps + 1
>
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
>
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
>
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
>
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
>
> # compute efficient score statistics
> res <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta)
> res
[,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,] 0.09537326
[6,] 0.50679716
[7,] -0.01163486
[8,] -0.02150784
>
>
>
> cleanEx()
Error: connections left open:
<-CRANwin.fb05.statistik.uni-dortmund.de:11982 (sockconn)
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 1.0.3
Check: package dependencies
Result: ERROR
Package required but not available: ‘qvalue’
Package suggested but not available for checking: ‘snplist’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-osx-x86_64