CRAN Package Check Results for Package frailtySurv

Last updated on 2018-05-25 22:47:42 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3.2 35.30 74.84 110.14 ERROR
r-devel-linux-x86_64-debian-gcc 1.3.2 27.51 59.74 87.25 ERROR
r-devel-linux-x86_64-fedora-clang 1.3.2 154.29 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3.2 140.88 NOTE
r-devel-windows-ix86+x86_64 1.3.2 69.00 125.00 194.00 OK
r-patched-linux-x86_64 1.3.2 35.46 64.49 99.95 ERROR
r-patched-solaris-x86 1.3.2 162.60 OK
r-release-linux-x86_64 1.3.2 30.39 64.04 94.43 ERROR
r-release-windows-ix86+x86_64 1.3.2 79.00 151.00 230.00 OK
r-release-osx-x86_64 1.3.2 OK
r-oldrel-windows-ix86+x86_64 1.3.2 93.00 116.00 209.00 OK
r-oldrel-osx-x86_64 1.3.2 OK

Check Details

Version: 1.3.2
Check: compiled code
Result: NOTE
    File ‘frailtySurv/libs/frailtySurv.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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: 1.3.2
Check: examples
Result: ERROR
    Running examples in ‘frailtySurv-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitfrail
    > ### Title: Fit a shared frailty model
    > ### Aliases: fitfrail
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D #
    > ##D # Generate synthetic survival data with regression coefficients
    > ##D # beta = c(log(2),log(3)) and theta = 2, where the shared frailty
    > ##D # values from a gamma distribution with expectation 1 and variance theta.
    > ##D #
    > ##D dat <- genfrail(N=300, K=2, beta=c(log(2),log(3)),
    > ##D frailty="gamma", theta=2,
    > ##D censor.rate=0.35,
    > ##D Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    > ##D
    > ##D # Fit a shared frailty model
    > ##D fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    > ##D dat, frailty="gamma")
    > ##D fit
    > ##D
    > ##D # The Lambda.fun function can give the estimated cumulative baseline hazard at
    > ##D # any time
    > ##D fit$Lambda.fun(seq(0, 100, by=10))
    > ##D
    > ##D # Fit the DRS data, clustered on patient
    > ##D data(drs)
    > ##D fit.drs <- fitfrail(Surv(time, status) ~ treated + cluster(subject_id),
    > ##D drs, frailty="gamma")
    > ##D fit.drs
    > ## End(Not run)
    >
    > #
    > # A small example with c(log(2),log(3)) coefficients, Gamma(2) frailty, and
    > # 0.10 censorship.
    > #
    > dat <- genfrail(N=30, K=2, beta=c(log(2),log(3)),
    + frailty="gamma", theta=2,
    + censor.rate=0.10,
    + Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    >
    > # Fit a shared frailty model
    > fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    + dat, frailty="gamma", se=TRUE)
    Warning in sqrt(fit$vcov) : NaNs produced
    > fit
    Call: fitfrail(formula = Surv(time, status) ~ Z1 + Z2 + cluster(family),
     dat = dat, frailty = "gamma", se = TRUE)
    
     Covariate Coefficient SE
     Z1 0.683 0.270
     Z2 1.255 0.377
    
    Frailty distribution gamma(1.669), VAR of frailty variates = 1.669
    Frailty parameter SE 0.988
    Log-likelihood -214.246
    Converged (method) 11 iterations, 0.414 secs (maximized log-likelihood)
    >
    > # Summarize the survival curve
    > head(summary(fit))
    Error in if (!match(type, c("survival", "cumhaz"), nomatch = 0)) stop("type must be either 'survival' or 'cumhaz'") :
     the condition has length > 1
    Calls: head -> summary -> summary.fitfrail
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.3.2
Check: examples
Result: ERROR
    Running examples in ‘frailtySurv-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitfrail
    > ### Title: Fit a shared frailty model
    > ### Aliases: fitfrail
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D #
    > ##D # Generate synthetic survival data with regression coefficients
    > ##D # beta = c(log(2),log(3)) and theta = 2, where the shared frailty
    > ##D # values from a gamma distribution with expectation 1 and variance theta.
    > ##D #
    > ##D dat <- genfrail(N=300, K=2, beta=c(log(2),log(3)),
    > ##D frailty="gamma", theta=2,
    > ##D censor.rate=0.35,
    > ##D Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    > ##D
    > ##D # Fit a shared frailty model
    > ##D fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    > ##D dat, frailty="gamma")
    > ##D fit
    > ##D
    > ##D # The Lambda.fun function can give the estimated cumulative baseline hazard at
    > ##D # any time
    > ##D fit$Lambda.fun(seq(0, 100, by=10))
    > ##D
    > ##D # Fit the DRS data, clustered on patient
    > ##D data(drs)
    > ##D fit.drs <- fitfrail(Surv(time, status) ~ treated + cluster(subject_id),
    > ##D drs, frailty="gamma")
    > ##D fit.drs
    > ## End(Not run)
    >
    > #
    > # A small example with c(log(2),log(3)) coefficients, Gamma(2) frailty, and
    > # 0.10 censorship.
    > #
    > dat <- genfrail(N=30, K=2, beta=c(log(2),log(3)),
    + frailty="gamma", theta=2,
    + censor.rate=0.10,
    + Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    >
    > # Fit a shared frailty model
    > fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    + dat, frailty="gamma", se=TRUE)
    Warning in sqrt(fit$vcov) : NaNs produced
    > fit
    Call: fitfrail(formula = Surv(time, status) ~ Z1 + Z2 + cluster(family),
     dat = dat, frailty = "gamma", se = TRUE)
    
     Covariate Coefficient SE
     Z1 0.683 0.270
     Z2 1.255 0.377
    
    Frailty distribution gamma(1.669), VAR of frailty variates = 1.669
    Frailty parameter SE 0.988
    Log-likelihood -214.246
    Converged (method) 11 iterations, 0.145 secs (maximized log-likelihood)
    >
    > # Summarize the survival curve
    > head(summary(fit))
    Error in if (!match(type, c("survival", "cumhaz"), nomatch = 0)) stop("type must be either 'survival' or 'cumhaz'") :
     the condition has length > 1
    Calls: head -> summary -> summary.fitfrail
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.3.2
Check: examples
Result: ERROR
    Running examples in ‘frailtySurv-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitfrail
    > ### Title: Fit a shared frailty model
    > ### Aliases: fitfrail
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D #
    > ##D # Generate synthetic survival data with regression coefficients
    > ##D # beta = c(log(2),log(3)) and theta = 2, where the shared frailty
    > ##D # values from a gamma distribution with expectation 1 and variance theta.
    > ##D #
    > ##D dat <- genfrail(N=300, K=2, beta=c(log(2),log(3)),
    > ##D frailty="gamma", theta=2,
    > ##D censor.rate=0.35,
    > ##D Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    > ##D
    > ##D # Fit a shared frailty model
    > ##D fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    > ##D dat, frailty="gamma")
    > ##D fit
    > ##D
    > ##D # The Lambda.fun function can give the estimated cumulative baseline hazard at
    > ##D # any time
    > ##D fit$Lambda.fun(seq(0, 100, by=10))
    > ##D
    > ##D # Fit the DRS data, clustered on patient
    > ##D data(drs)
    > ##D fit.drs <- fitfrail(Surv(time, status) ~ treated + cluster(subject_id),
    > ##D drs, frailty="gamma")
    > ##D fit.drs
    > ## End(Not run)
    >
    > #
    > # A small example with c(log(2),log(3)) coefficients, Gamma(2) frailty, and
    > # 0.10 censorship.
    > #
    > dat <- genfrail(N=30, K=2, beta=c(log(2),log(3)),
    + frailty="gamma", theta=2,
    + censor.rate=0.10,
    + Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    >
    > # Fit a shared frailty model
    > fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    + dat, frailty="gamma", se=TRUE)
    Warning in sqrt(fit$vcov) : NaNs produced
    > fit
    Call: fitfrail(formula = Surv(time, status) ~ Z1 + Z2 + cluster(family),
     dat = dat, frailty = "gamma", se = TRUE)
    
     Covariate Coefficient SE
     Z1 0.683 0.270
     Z2 1.255 0.377
    
    Frailty distribution gamma(1.669), VAR of frailty variates = 1.669
    Frailty parameter SE 0.988
    Log-likelihood -214.246
    Converged (method) 11 iterations, 0.209 secs (maximized log-likelihood)
    >
    > # Summarize the survival curve
    > head(summary(fit))
    Error in if (!match(type, c("survival", "cumhaz"), nomatch = 0)) stop("type must be either 'survival' or 'cumhaz'") :
     the condition has length > 1
    Calls: head -> summary -> summary.fitfrail
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.3.2
Check: examples
Result: ERROR
    Running examples in ‘frailtySurv-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitfrail
    > ### Title: Fit a shared frailty model
    > ### Aliases: fitfrail
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D #
    > ##D # Generate synthetic survival data with regression coefficients
    > ##D # beta = c(log(2),log(3)) and theta = 2, where the shared frailty
    > ##D # values from a gamma distribution with expectation 1 and variance theta.
    > ##D #
    > ##D dat <- genfrail(N=300, K=2, beta=c(log(2),log(3)),
    > ##D frailty="gamma", theta=2,
    > ##D censor.rate=0.35,
    > ##D Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    > ##D
    > ##D # Fit a shared frailty model
    > ##D fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    > ##D dat, frailty="gamma")
    > ##D fit
    > ##D
    > ##D # The Lambda.fun function can give the estimated cumulative baseline hazard at
    > ##D # any time
    > ##D fit$Lambda.fun(seq(0, 100, by=10))
    > ##D
    > ##D # Fit the DRS data, clustered on patient
    > ##D data(drs)
    > ##D fit.drs <- fitfrail(Surv(time, status) ~ treated + cluster(subject_id),
    > ##D drs, frailty="gamma")
    > ##D fit.drs
    > ## End(Not run)
    >
    > #
    > # A small example with c(log(2),log(3)) coefficients, Gamma(2) frailty, and
    > # 0.10 censorship.
    > #
    > dat <- genfrail(N=30, K=2, beta=c(log(2),log(3)),
    + frailty="gamma", theta=2,
    + censor.rate=0.10,
    + Lambda_0=function(t, tau=4.6, C=0.01) (C*t)^tau)
    >
    > # Fit a shared frailty model
    > fit <- fitfrail(Surv(time, status) ~ Z1 + Z2 + cluster(family),
    + dat, frailty="gamma", se=TRUE)
    Warning in sqrt(fit$vcov) : NaNs produced
    > fit
    Call: fitfrail(formula = Surv(time, status) ~ Z1 + Z2 + cluster(family),
     dat = dat, frailty = "gamma", se = TRUE)
    
     Covariate Coefficient SE
     Z1 0.683 0.270
     Z2 1.255 0.377
    
    Frailty distribution gamma(1.669), VAR of frailty variates = 1.669
    Frailty parameter SE 0.988
    Log-likelihood -214.246
    Converged (method) 11 iterations, 0.239 secs (maximized log-likelihood)
    >
    > # Summarize the survival curve
    > head(summary(fit))
    Error in if (!match(type, c("survival", "cumhaz"), nomatch = 0)) stop("type must be either 'survival' or 'cumhaz'") :
     the condition has length > 1
    Calls: head -> summary -> summary.fitfrail
    Execution halted
Flavor: r-release-linux-x86_64