CRAN Package Check Results for Package TimeMachine

Last updated on 2015-02-01 17:50:23.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 1.06 28.46 29.52 NOTE
r-devel-linux-x86_64-debian-gcc 1.2 1.12 25.96 27.08 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 59.23 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 57.74 NOTE
r-devel-osx-x86_64-clang 1.2 62.56 NOTE
r-devel-windows-ix86+x86_64 1.2 8.00 70.00 78.00 NOTE
r-patched-linux-x86_64 1.2 1.21 25.61 26.82 NOTE
r-patched-solaris-sparc 1.2 155.60 ERROR
r-patched-solaris-x86 1.2 40.60 ERROR
r-release-linux-ix86 1.2 1.63 39.40 41.03 NOTE
r-release-linux-x86_64 1.2 1.20 25.84 27.04 NOTE
r-release-osx-x86_64-mavericks 1.2 NOTE
r-release-osx-x86_64-snowleopard 1.2 NOTE
r-release-windows-ix86+x86_64 1.2 7.00 69.00 76.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2 7.00 69.00 76.00 NOTE

Check Details

Version: 1.2
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 1.2
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     mean.tm print.tm summary.tm density.tm quantile.tm
    See section ‘Registering S3 methods’ 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-devel-osx-x86_64-clang

Version: 1.2
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2
Check: examples
Result: ERROR
    Running examples in ‘TimeMachine-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mu.mle
    > ### Title: Maximum-Likelihood Estimation of the Mutation Rate
    > ### Aliases: mu.mle
    >
    > ### ** Examples
    >
    > # Load example dataset
    > data(pdm)
    > transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
    > pi <- stationary.dist(transitions)
    >
    > mu.int <- c(0.1, 10)
    > samples <- 10
    >
    > # MLE of the mutation rate for a single target population size
    > n <- 10
    > mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
    Error: C stack usage 83890436 is too close to the limit
    Execution halted
    Execution halted
    Execution halted
    Execution halted
    Execution halted
    Execution halted
    Execution halted
    
     *** caught segfault ***
    address 8, cause 'memory not mapped'
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: .Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads)
     2: structure(.Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads), class = "em")
    Traceback:
    
     1: 3: .Call("estimate_loglik", transitions, pi, population, n, mu, tm(transitions, pi, population, n, mu, samples, threads) samples, threads)
    
     4: 2: mean(tm(transitions, pi, population, n, mu, samples, threads))structure(.Call("estimate_loglik", transitions, pi, population,
     n, mu, samples, threads), class = "tm") 5:
    f(arg, ...) 3:
    tm(transitions, pi, population, n, mu, samples, threads) 6:
    (function (arg) 4: -f(arg, ...))(3.88146351137604)mean(tm(transitions, pi, population, n, mu, samples, threads))
    
     7: 5: optimize(function(mu) {f(arg, ...) mean(tm(transitions, pi, population, n, mu, samples, threads))
    }, mu.int, maximum = TRUE, ...)
     6: 8: (function (arg) mu.mle(transitions, pi, pdm$population, n, mu.int, samples)-f(arg, ...))(3.88146351137604)
    
     7: aborting ...
    optimize(function(mu) { mean(tm(transitions, pi, population, n, mu, samples, threads))}, mu.int, maximum = TRUE, ...)
     8: mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
    aborting ...
    rm: Unable to remove directory /tmp/RtmpJaa4r3: mp/RtmpJaa4r3: No such file or directory
Flavor: r-patched-solaris-sparc

Version: 1.2
Check: examples
Result: ERROR
    Running examples in ‘TimeMachine-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mu.mle
    > ### Title: Maximum-Likelihood Estimation of the Mutation Rate
    > ### Aliases: mu.mle
    >
    > ### ** Examples
    >
    > # Load example dataset
    > data(pdm)
    > transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
    > pi <- stationary.dist(transitions)
    >
    > mu.int <- c(0.1, 10)
    > samples <- 10
    >
    > # MLE of the mutation rate for a single target population size
    > n <- 10
    > mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
    Warning in structure(.Call("estimate_loglik", transitions, pi, population, :
     value out of range in 'lgamma'
    Warning in structure(.Call("estimate_loglik", transitions, pi, population, :
     value out of range in 'lgamma'
    Warning in structure(.Call("estimate_loglik", transitions, pi, population, :
     value out of range in 'lgamma'
    Warning in optimize(function(mu) { :
     NA/Inf replaced by maximum positive value
    
     *** caught segfault ***
    address 1, cause 'memory not mapped'
    Warning in structure(.Call("estimate_loglik", transitions, pi, population, :
     value out of range in 'lgamma'
    
     *** caught segfault ***
    address 3efa8ac6, cause 'memory not mapped'
    
    Traceback:
     1: doWithOneRestart(return(expr), restart)
     2: withOneRestart(expr, restarts[[1L]])
     3: withRestarts({ .Internal(.signalCondition(simpleWarning(msg, call), msg, call)) .Internal(.dfltWarn(msg, call))}, muffleWarning = function() NULL)
     4: .signalSimpleWarning("value out of range in 'lgamma'", quote(structure(.Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads), class = "tm")))
     5: .Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads)
     6: structure(.Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads), class = "tm")
     7: tm(transitions, pi, population, n, mu, samples, threads)
     8: mean(tm(transitions, pi, population, n, mu, samples, threads))
     9: f(arg, ...)
    10: (function (arg) -f(arg, ...))(6.21853648862396)
    11: optimize(function(mu) { mean(tm(transitions, pi, population, n, mu, samples, threads))}, mu.int, maximum = TRUE, ...)
    12: mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
    aborting ...
    
    Traceback:
     1: match(names(attrib), specials)
     2: structure(list(message = as.character(message), call = call), class = class)
     3: simpleWarning(msg, call)
     4: doWithOneRestart(return(expr), restart)
     5: withOneRestart(expr, restarts[[1L]])
     6: withRestarts({ .Internal(.signalCondition(simpleWarning(msg, call), msg, call)) .Internal(.dfltWarn(msg, call))}, muffleWarning = function() NULL)
     7: .signalSimpleWarning("value out of range in 'lgamma'", quote(withOneRestart(expr, restarts[[1L]])))
     8: .Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads)
     9: structure(.Call("estimate_loglik", transitions, pi, population, n, mu, samples, threads), class = "tm")
    10: tm(transitions, pi, population, n, mu, samples, threads)
    11: mean(tm(transitions, pi, population, n, mu, samples, threads))
    12: f(arg, ...)
    13: (function (arg) -f(arg, ...))(6.21853648862396)
    14: optimize(function(mu) { mean(tm(transitions, pi, population, n, mu, samples, threads))}, mu.int, maximum = TRUE, ...)
    15: mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
    aborting ...
Flavor: r-patched-solaris-x86

Version: 1.2
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘methods’
     These packages need to be imported from for the case when
     this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-release-osx-x86_64-snowleopard