CRAN Package Check Results for Package phase1RMD

Last updated on 2020-02-26 10:48:26 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.8 10.37 60.91 71.28 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.8 7.73 46.81 54.54 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.8 82.26 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.8 80.18 ERROR
r-devel-windows-ix86+x86_64 1.0.8 16.00 76.00 92.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.8 18.00 80.00 98.00 OK
r-patched-linux-x86_64 1.0.8 7.48 60.20 67.68 OK
r-patched-solaris-x86 1.0.8 129.10 OK
r-release-linux-x86_64 1.0.8 8.53 60.08 68.61 OK
r-release-windows-ix86+x86_64 1.0.8 14.00 71.00 85.00 OK
r-release-osx-x86_64 1.0.8 NOTE
r-oldrel-windows-ix86+x86_64 1.0.8 12.00 72.00 84.00 OK
r-oldrel-osx-x86_64 1.0.8 OK

Check Details

Version: 1.0.8
Check: examples
Result: ERROR
    Running examples in 'phase1RMD-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: RunRMD
    > ### Title: Toxicity-based Dose estimation for the next patient cohort.
    > ### Aliases: RunRMD
    >
    > ### ** Examples
    >
    > # Setup the prior distributions for the phase I dose-finding model:
    > control <- list(
    + beta.dose = parm("normal", mean = 0, var = 1000),
    + beta.other = parm("normal", mean = 0, var = 1000 ),
    + gamma = parm("normal", mean = 0, var = 100 ),
    + s2.gamma = parm("invgamma", shape = 0.001, scale = 0.001),
    + s2.epsilon = parm("invgamma", shape = 0.001, scale = 0.001)
    + )
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    phase1RMD
     --- call from context ---
    parm("normal", mean = 0, var = 1000)
     --- call from argument ---
    if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     --- R stacktrace ---
    where 1: parm("normal", mean = 0, var = 1000)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (prior = c("gamma", "invgamma", "normal"), mean = 0,
     var = 100, shape = 0.001, scale = 0.001)
    {
     monitor <- TRUE
     tuning <- NULL
     if (any(tuning <= 0))
     stop("Tuning values must be positive")
     if (!is.logical(monitor))
     stop("Monitor value must be a logical")
     retval <- list()
     retval$prior <- match.arg(prior)
     retval$monitor <- monitor
     retval$tuning <- tuning
     hyper <- list(mean = mean, var = var, shape = shape, scale = scale)
     switch(retval$prior, gamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$rate) || hyper$rate <= 0) stop("Gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$rate <- hyper$rate
     }, invgamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Inverse gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$scale) || hyper$scale <= 0) stop("Inverse gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$scale <- hyper$scale
     }, normal = {
     if (!is.numeric(hyper$mean)) stop("Normal mean hyperparameter must be numeric")
     if (!is.numeric(hyper$var)) stop("Normal variance hyperparameter must be numeric")
     retval$mean <- hyper$mean
     retval$var <- hyper$var
     val <- try(chol(retval$var))
     if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     retval$prec <- chol2inv(val)
     dim(retval$prec) <- dim(retval$var)
     })
     structure(retval, class = "parm")
    }
    <bytecode: 0x5ca9810>
    <environment: namespace:phase1RMD>
     --- function search by body ---
    Function parm in namespace phase1RMD has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite") :
     the condition has length > 1
    Calls: parm
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.8
Check: examples
Result: ERROR
    Running examples in ‘phase1RMD-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: RunRMD
    > ### Title: Toxicity-based Dose estimation for the next patient cohort.
    > ### Aliases: RunRMD
    >
    > ### ** Examples
    >
    > # Setup the prior distributions for the phase I dose-finding model:
    > control <- list(
    + beta.dose = parm("normal", mean = 0, var = 1000),
    + beta.other = parm("normal", mean = 0, var = 1000 ),
    + gamma = parm("normal", mean = 0, var = 100 ),
    + s2.gamma = parm("invgamma", shape = 0.001, scale = 0.001),
    + s2.epsilon = parm("invgamma", shape = 0.001, scale = 0.001)
    + )
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    phase1RMD
     --- call from context ---
    parm("normal", mean = 0, var = 1000)
     --- call from argument ---
    if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     --- R stacktrace ---
    where 1: parm("normal", mean = 0, var = 1000)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (prior = c("gamma", "invgamma", "normal"), mean = 0,
     var = 100, shape = 0.001, scale = 0.001)
    {
     monitor <- TRUE
     tuning <- NULL
     if (any(tuning <= 0))
     stop("Tuning values must be positive")
     if (!is.logical(monitor))
     stop("Monitor value must be a logical")
     retval <- list()
     retval$prior <- match.arg(prior)
     retval$monitor <- monitor
     retval$tuning <- tuning
     hyper <- list(mean = mean, var = var, shape = shape, scale = scale)
     switch(retval$prior, gamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$rate) || hyper$rate <= 0) stop("Gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$rate <- hyper$rate
     }, invgamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Inverse gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$scale) || hyper$scale <= 0) stop("Inverse gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$scale <- hyper$scale
     }, normal = {
     if (!is.numeric(hyper$mean)) stop("Normal mean hyperparameter must be numeric")
     if (!is.numeric(hyper$var)) stop("Normal variance hyperparameter must be numeric")
     retval$mean <- hyper$mean
     retval$var <- hyper$var
     val <- try(chol(retval$var))
     if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     retval$prec <- chol2inv(val)
     dim(retval$prec) <- dim(retval$var)
     })
     structure(retval, class = "parm")
    }
    <bytecode: 0x562492163d08>
    <environment: namespace:phase1RMD>
     --- function search by body ---
    Function parm in namespace phase1RMD has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite") :
     the condition has length > 1
    Calls: parm
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.8
Check: examples
Result: ERROR
    Running examples in ‘phase1RMD-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: RunRMD
    > ### Title: Toxicity-based Dose estimation for the next patient cohort.
    > ### Aliases: RunRMD
    >
    > ### ** Examples
    >
    > # Setup the prior distributions for the phase I dose-finding model:
    > control <- list(
    + beta.dose = parm("normal", mean = 0, var = 1000),
    + beta.other = parm("normal", mean = 0, var = 1000 ),
    + gamma = parm("normal", mean = 0, var = 100 ),
    + s2.gamma = parm("invgamma", shape = 0.001, scale = 0.001),
    + s2.epsilon = parm("invgamma", shape = 0.001, scale = 0.001)
    + )
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    phase1RMD
     --- call from context ---
    parm("normal", mean = 0, var = 1000)
     --- call from argument ---
    if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     --- R stacktrace ---
    where 1: parm("normal", mean = 0, var = 1000)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (prior = c("gamma", "invgamma", "normal"), mean = 0,
     var = 100, shape = 0.001, scale = 0.001)
    {
     monitor <- TRUE
     tuning <- NULL
     if (any(tuning <= 0))
     stop("Tuning values must be positive")
     if (!is.logical(monitor))
     stop("Monitor value must be a logical")
     retval <- list()
     retval$prior <- match.arg(prior)
     retval$monitor <- monitor
     retval$tuning <- tuning
     hyper <- list(mean = mean, var = var, shape = shape, scale = scale)
     switch(retval$prior, gamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$rate) || hyper$rate <= 0) stop("Gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$rate <- hyper$rate
     }, invgamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Inverse gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$scale) || hyper$scale <= 0) stop("Inverse gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$scale <- hyper$scale
     }, normal = {
     if (!is.numeric(hyper$mean)) stop("Normal mean hyperparameter must be numeric")
     if (!is.numeric(hyper$var)) stop("Normal variance hyperparameter must be numeric")
     retval$mean <- hyper$mean
     retval$var <- hyper$var
     val <- try(chol(retval$var))
     if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     retval$prec <- chol2inv(val)
     dim(retval$prec) <- dim(retval$var)
     })
     structure(retval, class = "parm")
    }
    <bytecode: 0x630d070>
    <environment: namespace:phase1RMD>
     --- function search by body ---
    Function parm in namespace phase1RMD has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite") :
     the condition has length > 1
    Calls: parm
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.8
Check: examples
Result: ERROR
    Running examples in ‘phase1RMD-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: RunRMD
    > ### Title: Toxicity-based Dose estimation for the next patient cohort.
    > ### Aliases: RunRMD
    >
    > ### ** Examples
    >
    > # Setup the prior distributions for the phase I dose-finding model:
    > control <- list(
    + beta.dose = parm("normal", mean = 0, var = 1000),
    + beta.other = parm("normal", mean = 0, var = 1000 ),
    + gamma = parm("normal", mean = 0, var = 100 ),
    + s2.gamma = parm("invgamma", shape = 0.001, scale = 0.001),
    + s2.epsilon = parm("invgamma", shape = 0.001, scale = 0.001)
    + )
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    phase1RMD
     --- call from context ---
    parm("normal", mean = 0, var = 1000)
     --- call from argument ---
    if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     --- R stacktrace ---
    where 1: parm("normal", mean = 0, var = 1000)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (prior = c("gamma", "invgamma", "normal"), mean = 0,
     var = 100, shape = 0.001, scale = 0.001)
    {
     monitor <- TRUE
     tuning <- NULL
     if (any(tuning <= 0))
     stop("Tuning values must be positive")
     if (!is.logical(monitor))
     stop("Monitor value must be a logical")
     retval <- list()
     retval$prior <- match.arg(prior)
     retval$monitor <- monitor
     retval$tuning <- tuning
     hyper <- list(mean = mean, var = var, shape = shape, scale = scale)
     switch(retval$prior, gamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$rate) || hyper$rate <= 0) stop("Gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$rate <- hyper$rate
     }, invgamma = {
     if (!is.numeric(hyper$shape) || hyper$shape <= 0) stop("Inverse gamma shape hyperparameter must be numeric > 0")
     if (!is.numeric(hyper$scale) || hyper$scale <= 0) stop("Inverse gamma scale hyperparameter must be numeric > 0")
     retval$shape <- hyper$shape
     retval$scale <- hyper$scale
     }, normal = {
     if (!is.numeric(hyper$mean)) stop("Normal mean hyperparameter must be numeric")
     if (!is.numeric(hyper$var)) stop("Normal variance hyperparameter must be numeric")
     retval$mean <- hyper$mean
     retval$var <- hyper$var
     val <- try(chol(retval$var))
     if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite")
     retval$prec <- chol2inv(val)
     dim(retval$prec) <- dim(retval$var)
     })
     structure(retval, class = "parm")
    }
    <bytecode: 0x5765450>
    <environment: namespace:phase1RMD>
     --- function search by body ---
    Function parm in namespace phase1RMD has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(val) == "try-error") stop("Normal variance hyperparameter must be positive definite") :
     the condition has length > 1
    Calls: parm
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.8
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘BiocParallel’
Flavor: r-release-osx-x86_64