CRAN Package Check Results for Package pegas

Last updated on 2020-02-21 05:47:18 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.12 26.22 194.01 220.23 ERROR
r-devel-linux-x86_64-debian-gcc 0.12 22.21 151.29 173.50 OK
r-devel-linux-x86_64-fedora-clang 0.12 265.79 OK
r-devel-linux-x86_64-fedora-gcc 0.12 263.54 OK
r-devel-windows-ix86+x86_64 0.12 52.00 269.00 321.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.12 67.00 304.00 371.00 OK
r-patched-linux-x86_64 0.12 23.91 174.48 198.39 OK
r-patched-solaris-x86 0.12 381.90 OK
r-release-linux-x86_64 0.12 24.66 174.89 199.55 OK
r-release-windows-ix86+x86_64 0.12 45.00 240.00 285.00 OK
r-release-osx-x86_64 0.12 NOTE
r-oldrel-windows-ix86+x86_64 0.12 33.00 212.00 245.00 OK
r-oldrel-osx-x86_64 0.12 NOTE

Check Details

Version: 0.12
Check: examples
Result: ERROR
    Running examples in 'pegas-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: amova
    > ### Title: Analysis of Molecular Variance
    > ### Aliases: amova print.amova getPhi write.pegas.amova
    > ### Keywords: models
    >
    > ### ** Examples
    >
    > ### All examples below have 'nperm = 100' for faster execution times.
    > ### The default 'nperm = 1000' is recommended.
    > require(ape)
    > data(woodmouse)
    > d <- dist.dna(woodmouse)
    > g <- factor(c(rep("A", 7), rep("B", 8)))
    > p <- factor(c(rep(1, 3), rep(2, 4), rep(3, 4), rep(4, 4)))
    > (d_gp <- amova(d ~ g/p, nperm = 100)) # 2 levels
    Error in FUN(X[[i]], ...) : 'bin' must be numeric or a factor
    Calls: amova -> lapply -> FUN
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.12
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'ReadingFiles.Rnw' using Sweave
    Loading required package: ape
    Loading required package: adegenet
    Loading required package: ade4
    
     /// adegenet 2.1.2 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    Registered S3 method overwritten by 'pegas':
     method from
     print.amova ade4
    
    Attaching package: 'pegas'
    
    The following object is masked from 'package:ade4':
    
     amova
    
    The following object is masked from 'package:ape':
    
     mst
    
    
    Error: processing vignette 'ReadingFiles.Rnw' failed with diagnostics:
     chunk 6
    Error in summary.loci(X) :
     INTEGER() can only be applied to a 'integer', not a 'character'
    
    --- failed re-building 'ReadingFiles.Rnw'
    
    SUMMARY: processing the following file failed:
     'ReadingFiles.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.12
Check: dependencies in R code
Result: NOTE
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64