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 |
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