CRAN Package Check Results for Package RPANDA

Last updated on 2019-11-26 00:52:09 CET.

Check Details

Version: 1.6
Check: examples
Result: ERROR
    Running examples in 'RPANDA-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitTipData
    > ### Title: Maximum likelihood estimators of a model's parameters
    > ### Aliases: fitTipData
    >
    > ### ** Examples
    >
    > #Loading an example tree
    > newick <- "((((A:1,B:0.5):2,(C:3,D:2.5):1):6,E:10.25):2,(F:6.5,G:8.25):3):1;"
    > tree <- read.tree(text=newick)
    >
    > #Creating the models
    > modelBM <- createModel(tree, 'BM')
    >
    > #Simulating tip traits under the model :
    > dataBM <- simulateTipData(modelBM, c(0,0,0,1))
    *** Simulation of tip trait values ***
    Simulates step-by-step the whole trajectory, but returns only the tip data.
    Computation time : 0.7148261 secs
    >
    > #Fitting the model to the data
    > fitTipData(modelBM, dataBM, v=TRUE)
    *** Fit of tip trait data ***
    Finds the maximum likelihood estimators of the parameters,
    returns the likelihood and the inferred parameters.
    **WARNING** : This function uses the standard R optimizer "optim".
    It may not always converge well.
    Please double check the convergence by trying
    distinct parameter sets for the initialisation.
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    RPANDA
     --- call from context ---
    getDataLikelihood(object, data, params)
     --- call from argument ---
    if (class(IV) == "try-error") {
     IV = pseudoinverse(V)
     if (max(IV) == 0) {
     return(Inf)
     }
    }
     --- R stacktrace ---
    where 1: getDataLikelihood(object, data, params)
    where 2: getDataLikelihood(object, data, params)
    where 3: fn(par, ...)
    where 4: (function (par)
    fn(par, ...))(c(0, 0, 0, 1))
    where 5: optim(params0, toBeOptimized)
    where 6: fitTipData(modelBM, dataBM, v = TRUE)
    where 7: fitTipData(modelBM, dataBM, v = TRUE)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    Method Definition:
    
    function (object = "PhenotypicModel", data = "numeric", params = "numeric",
     v = FALSE)
    {
     if (v) {
     cat("*** Computing -log( likelihood ) of tip trait data under a given set of parameters ***\n")
     beginning <- Sys.time()
     }
     if (!is.null(rownames(data))) {
     data <- data[object@tipLabels, ]
     }
     if (object@constraints(params)) {
     n <- length(data)
     tipdistribution <- getTipDistribution(object, params)
     V <- tipdistribution$Sigma
     data <- data[rownames(V)]
     op <- getOption("show.error.messages")
     options(show.error.messages = FALSE)
     IV = try(solve(V))
     options(show.error.messages = op)
     if (class(IV) == "try-error") {
     IV = pseudoinverse(V)
     if (max(IV) == 0) {
     return(Inf)
     }
     }
     dataminusXT <- matrix(data - tipdistribution$mean, nrow = 1)
     dataminusX <- matrix(data - tipdistribution$mean, ncol = 1)
     ProdVectoriel = dataminusXT %*% IV %*% dataminusX
     calcul <- (ProdVectoriel + determinant(V)$modulus + n *
     log(2 * pi))/2
     if (is.na(calcul) | is.infinite(calcul)) {
     calcul = -1e+06
     }
     }
     else {
     calcul <- -Inf
     }
     if (v) {
     end <- Sys.time()
     cat("Computation time :", format(end - beginning), "\n")
     }
     return(as.numeric(calcul))
    }
    <bytecode: 0x12d5f610>
    <environment: namespace:RPANDA>
    
    Signatures:
     object
    target "PhenotypicBM"
    defined "PhenotypicModel"
     --- function search by body ---
    S4 Method getDataLikelihood:RPANDA defined in namespace RPANDA with signature PhenotypicModel has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.6
Check: examples
Result: ERROR
    Running examples in ‘RPANDA-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fitTipData
    > ### Title: Maximum likelihood estimators of a model's parameters
    > ### Aliases: fitTipData
    >
    > ### ** Examples
    >
    > #Loading an example tree
    > newick <- "((((A:1,B:0.5):2,(C:3,D:2.5):1):6,E:10.25):2,(F:6.5,G:8.25):3):1;"
    > tree <- read.tree(text=newick)
    >
    > #Creating the models
    > modelBM <- createModel(tree, 'BM')
    >
    > #Simulating tip traits under the model :
    > dataBM <- simulateTipData(modelBM, c(0,0,0,1))
    *** Simulation of tip trait values ***
    Simulates step-by-step the whole trajectory, but returns only the tip data.
    Computation time : 0.4386101 secs
    >
    > #Fitting the model to the data
    > fitTipData(modelBM, dataBM, v=TRUE)
    *** Fit of tip trait data ***
    Finds the maximum likelihood estimators of the parameters,
    returns the likelihood and the inferred parameters.
    **WARNING** : This function uses the standard R optimizer "optim".
    It may not always converge well.
    Please double check the convergence by trying
    distinct parameter sets for the initialisation.
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    RPANDA
     --- call from context ---
    getDataLikelihood(object, data, params)
     --- call from argument ---
    if (class(IV) == "try-error") {
     IV = pseudoinverse(V)
     if (max(IV) == 0) {
     return(Inf)
     }
    }
     --- R stacktrace ---
    where 1: getDataLikelihood(object, data, params)
    where 2: getDataLikelihood(object, data, params)
    where 3: fn(par, ...)
    where 4: (function (par)
    fn(par, ...))(c(0, 0, 0, 1))
    where 5: optim(params0, toBeOptimized)
    where 6: fitTipData(modelBM, dataBM, v = TRUE)
    where 7: fitTipData(modelBM, dataBM, v = TRUE)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    Method Definition:
    
    function (object = "PhenotypicModel", data = "numeric", params = "numeric",
     v = FALSE)
    {
     if (v) {
     cat("*** Computing -log( likelihood ) of tip trait data under a given set of parameters ***\n")
     beginning <- Sys.time()
     }
     if (!is.null(rownames(data))) {
     data <- data[object@tipLabels, ]
     }
     if (object@constraints(params)) {
     n <- length(data)
     tipdistribution <- getTipDistribution(object, params)
     V <- tipdistribution$Sigma
     data <- data[rownames(V)]
     op <- getOption("show.error.messages")
     options(show.error.messages = FALSE)
     IV = try(solve(V))
     options(show.error.messages = op)
     if (class(IV) == "try-error") {
     IV = pseudoinverse(V)
     if (max(IV) == 0) {
     return(Inf)
     }
     }
     dataminusXT <- matrix(data - tipdistribution$mean, nrow = 1)
     dataminusX <- matrix(data - tipdistribution$mean, ncol = 1)
     ProdVectoriel = dataminusXT %*% IV %*% dataminusX
     calcul <- (ProdVectoriel + determinant(V)$modulus + n *
     log(2 * pi))/2
     if (is.na(calcul) | is.infinite(calcul)) {
     calcul = -1e+06
     }
     }
     else {
     calcul <- -Inf
     }
     if (v) {
     end <- Sys.time()
     cat("Computation time :", format(end - beginning), "\n")
     }
     return(as.numeric(calcul))
    }
    <bytecode: 0x555c9c6de868>
    <environment: namespace:RPANDA>
    
    Signatures:
     object
    target "PhenotypicBM"
    defined "PhenotypicModel"
     --- function search by body ---
    S4 Method getDataLikelihood:RPANDA defined in namespace RPANDA with signature PhenotypicModel has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.6
Check: compiled code
Result: NOTE
    File ‘RPANDA/libs/RPANDA.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-fedora-clang, r-devel-linux-x86_64-fedora-gcc