CRAN Package Check Results for Package TimeMachine

Last updated on 2015-06-30 15:47:30.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 0.99 25.50 26.48 NOTE
r-devel-linux-x86_64-debian-gcc 1.2 1.06 25.10 26.16 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 53.49 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 57.22 NOTE
r-devel-osx-x86_64-clang 1.2 54.14 NOTE
r-devel-windows-ix86+x86_64 1.2 13.00 72.00 85.00 NOTE
r-patched-linux-x86_64 1.2 1.12 25.77 26.88 NOTE
r-patched-solaris-sparc 1.2 161.00 ERROR
r-patched-solaris-x86 1.2 112.70 NOTE
r-release-linux-x86_64 1.2 1.09 25.55 26.64 NOTE
r-release-osx-x86_64-mavericks 1.2 NOTE
r-release-windows-ix86+x86_64 1.2 5.00 87.00 92.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2 12.00 73.00 85.00 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, r-patched-solaris-sparc, r-patched-solaris-x86, 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: 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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.2
Check: R code for possible problems
Result: NOTE
    density.tm: no visible global function definition for ‘density’
    mu.mle: no visible global function definition for ‘optimize’
    pophistory.tm: no visible binding for global variable ‘quantile’
    quantile.tm: no visible global function definition for ‘quantile’
    sample.pop: no visible global function definition for ‘runif’
    summary.tm: no visible global function definition for ‘quantile’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang

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 117444724 is too close to the limitError: C stack usage 117444724 is too close to the limit
    Execution halted
    Execution halted
    Execution halted
    Execution halted
    Error: C stack usage 117444724 is too close to the limit
    Execution halted
    Execution halted
    Error: C stack usage 117444724 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/Rtmp._aqNq: mp/Rtmp._aqNq: mp/Rtmp._aqNq: No such file or directory
Flavor: r-patched-solaris-sparc