CRAN Package Check Results for Package TimeMachine

Last updated on 2015-02-27 15:47:55.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 1.00 26.40 27.41 NOTE
r-devel-linux-x86_64-debian-gcc 1.2 1.06 25.36 26.42 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 55.00 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 55.21 NOTE
r-devel-osx-x86_64-clang 1.2 56.60 NOTE
r-devel-windows-ix86+x86_64 1.2 7.00 70.00 77.00 NOTE
r-patched-linux-x86_64 1.2 1.15 26.30 27.45 NOTE
r-patched-solaris-sparc 1.2 155.60 ERROR
r-release-linux-ix86 1.2 1.75 39.63 41.38 NOTE
r-release-linux-x86_64 1.2 1.16 26.24 27.40 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, r-patched-linux-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

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-solaris-sparc, 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: 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