CRAN Package Check Results for Package TimeMachine

Last updated on 2015-04-02 05:49:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 1.01 26.66 27.67 NOTE
r-devel-linux-x86_64-debian-gcc 1.2 1.15 24.64 25.79 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 53.46 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 54.84 NOTE
r-devel-osx-x86_64-clang 1.2 59.82 NOTE
r-prerel-windows-ix86+x86_64 1.2 9.00 77.00 86.00 NOTE
r-prerel-linux-x86_64 1.2 1.10 25.37 26.47 NOTE
r-prerel-solaris-sparc 1.2 175.40 ERROR
r-prerel-solaris-x86 1.2 212.00 NOTE
r-release-linux-x86_64 1.2 1.13 25.91 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 12.00 73.00 85.00 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-prerel-windows-ix86+x86_64, r-prerel-linux-x86_64, r-prerel-solaris-sparc, r-prerel-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 1.2
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     density.tm mean.tm print.tm quantile.tm summary.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, r-prerel-linux-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 67113156 is too close to the limit
    
    Error: C stack usage 83890372 is too close to the limit
    Execution halted
    Execution halted
    Error: C stack usage 83890372 is too close to the limit
    Execution halted
    Execution halted
    Execution halted
    Error: C stack usage 83890372 is too close to the limit
    Execution halted
    
     *** caught segfault ***
    address 8, 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 = "tm")
     3: tm(transitions, pi, population, n, mu, samples, threads)
     4: mean(tm(transitions, pi, population, n, mu, samples, threads))
     5: f(arg, ...)
     6: (function (arg) -f(arg, ...))(3.88146351137604)
     7: 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/Rtmp7uaOYd: No such file or directory
Flavor: r-prerel-solaris-sparc

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-release-osx-x86_64-mavericks, r-oldrel-windows-ix86+x86_64

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