CRAN Package Check Results for Package groupedSurv

Last updated on 2019-04-13 01:58:04 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 87.41 66.33 153.74 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.3 65.86 52.08 117.94 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.3 231.36 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.3 200.01 NOTE
r-devel-windows-ix86+x86_64 1.0.3 234.00 193.00 427.00 ERROR
r-patched-linux-x86_64 1.0.3 76.54 65.55 142.09 NOTE
r-patched-solaris-x86 1.0.3 225.70 OK
r-release-linux-x86_64 1.0.3 77.35 67.95 145.30 OK
r-release-windows-ix86+x86_64 1.0.3 245.00 210.00 455.00 OK
r-release-osx-x86_64 1.0.3 NOTE
r-oldrel-windows-ix86+x86_64 1.0.3 169.00 151.00 320.00 OK
r-oldrel-osx-x86_64 1.0.3 NOTE

Additional issues

clang-UBSAN

Check Details

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

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-release-osx-x86_64, 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:11190 (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:11261 (sockconn)
    Execution halted
Flavor: r-devel-windows-ix86+x86_64