CRAN Package Check Results for Package TimeMachine

Last updated on 2018-04-26 06:47:59 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 1.58 34.26 35.84 ERROR
r-devel-linux-x86_64-debian-gcc 1.2 1.49 26.09 27.58 ERROR
r-devel-linux-x86_64-fedora-clang 1.2 57.54 WARN
r-devel-linux-x86_64-fedora-gcc 1.2 56.27 NOTE
r-devel-windows-ix86+x86_64 1.2 12.00 88.00 100.00 NOTE
r-patched-linux-x86_64 1.2 1.89 35.33 37.22 ERROR
r-patched-solaris-x86 1.2 50.40 ERROR
r-release-linux-x86_64 1.2 1.53 38.12 39.65 ERROR
r-release-windows-ix86+x86_64 1.2 12.00 88.00 100.00 NOTE
r-release-osx-x86_64 1.2 WARN
r-oldrel-windows-ix86+x86_64 1.2 9.00 88.00 97.00 NOTE
r-oldrel-osx-x86_64 1.2 NOTE

Check Details

Version: 1.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
     tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-osx-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 (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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-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-patched-linux-x86_64, 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’
    Undefined global functions or variables:
     density optimize quantile runif
    Consider adding
     importFrom("stats", "density", "optimize", "quantile", "runif")
    to your NAMESPACE file.
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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.2
Check: compiled code
Result: NOTE
    File ‘TimeMachine/libs/TimeMachine.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-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.2
Check: examples
Result: ERROR
    Running examples in ‘TimeMachine-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: pophistory
    > ### Title: History of Population Size
    > ### Aliases: pophistory pophistory.tm
    >
    > ### ** Examples
    >
    > # Load example dataset
    > data(pdm)
    >
    > transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
    > pi <- stationary.dist(transitions)
    > n <- 10
    > mu <- 1
    > samples <- 10
    > est.res <- tm(transitions, pi, pdm$population, n, mu, samples)
    >
    > # Plot minimum, median and maximum SEN as a function of population size
    > h <- pophistory(est.res, probs=c(0, 0.5, 1))
    Error in UseMethod("pophistory") :
     no applicable method for 'pophistory' applied to an object of class "tm"
    Calls: pophistory -> pophistory
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-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 189040340 is too close to the limit
    Execution halted
Flavor: r-patched-solaris-x86