CRAN Package Check Results for Package pegas

Last updated on 2015-04-27 23:47:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.7 3.06 35.09 38.15 ERROR
r-devel-linux-x86_64-debian-gcc 0.7 2.37 34.28 36.65 ERROR
r-devel-linux-x86_64-fedora-clang 0.7 76.35 ERROR
r-devel-linux-x86_64-fedora-gcc 0.7 68.80 ERROR
r-devel-osx-x86_64-clang 0.7 71.60 ERROR
r-devel-windows-ix86+x86_64 0.7 10.00 70.00 80.00 ERROR
r-patched-linux-x86_64 0.7 2.36 39.16 41.52 OK
r-patched-solaris-sparc 0.7 557.40 OK
r-patched-solaris-x86 0.7 113.80 OK
r-release-linux-x86_64 0.7 2.25 39.51 41.76 OK
r-release-osx-x86_64-mavericks 0.7 OK
r-release-osx-x86_64-snowleopard 0.7 ERROR
r-release-windows-ix86+x86_64 0.7 17.00 114.00 131.00 OK
r-oldrel-windows-ix86+x86_64 0.7 12.00 121.00 133.00 OK

Check Details

Version: 0.7
Check: examples
Result: ERROR
    Running examples in ‘pegas-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: as.loci
    > ### Title: Conversion Among Allelic Data Classes
    > ### Aliases: as.loci as.loci.genind as.loci.data.frame as.loci.factor
    > ### as.loci.character genind2loci loci2genind
    > ### Keywords: IO
    >
    > ### ** Examples
    >
    > x <- c("A-A", "A-a", "a-a")
    > as.loci(x, allele.sep = "-")
    Allelic data frame: 3 individuals
     1 locus
    > require(adegenet)
    > data(nancycats)
    > x <- as.loci(nancycats)
    > y <- loci2genind(x) # back to "genind"
    Error in while (keepCheck) { : missing value where TRUE/FALSE needed
    Calls: loci2genind -> df2genind -> lapply -> FUN -> fillWithZero
    Execution halted
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: 0.7
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in ‘ReadingFiles.Rnw’
     ...
    
    > file.copy(system.file("files/nancycats.str", package = "adegenet"),
    + getwd())
    [1] TRUE
    
    > A <- read.fstat("nancycats.dat", quiet = TRUE)
    
     When sourcing ‘ReadingFiles.R’:
    Error: missing value where TRUE/FALSE needed
    Execution halted
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

Version: 0.7
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
     ==========================
     adegenet 1.4-2 is loaded
     ==========================
    
     - to start, type '?adegenet'
     - to browse adegenet website, type 'adegenetWeb()'
     - to post questions/comments: adegenet-forum@lists.r-forge.r-project.org
    
    
    
    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 13
    Error in while (keepCheck) { : missing value where TRUE/FALSE needed
    Execution halted
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

Version: 0.7
Check: running examples for arch 'i386'
Result: ERROR
    Running examples in 'pegas-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: as.loci
    > ### Title: Conversion Among Allelic Data Classes
    > ### Aliases: as.loci as.loci.genind as.loci.data.frame as.loci.factor
    > ### as.loci.character genind2loci loci2genind
    > ### Keywords: IO
    >
    > ### ** Examples
    >
    > x <- c("A-A", "A-a", "a-a")
    > as.loci(x, allele.sep = "-")
    Allelic data frame: 3 individuals
     1 locus
    > require(adegenet)
    > data(nancycats)
    > x <- as.loci(nancycats)
    > y <- loci2genind(x) # back to "genind"
    Error in while (keepCheck) { : missing value where TRUE/FALSE needed
    Calls: loci2genind -> df2genind -> lapply -> FUN -> fillWithZero
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.7
Check: running examples for arch 'x64'
Result: ERROR
    Running examples in 'pegas-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: as.loci
    > ### Title: Conversion Among Allelic Data Classes
    > ### Aliases: as.loci as.loci.genind as.loci.data.frame as.loci.factor
    > ### as.loci.character genind2loci loci2genind
    > ### Keywords: IO
    >
    > ### ** Examples
    >
    > x <- c("A-A", "A-a", "a-a")
    > as.loci(x, allele.sep = "-")
    Allelic data frame: 3 individuals
     1 locus
    > require(adegenet)
    > data(nancycats)
    > x <- as.loci(nancycats)
    > y <- loci2genind(x) # back to "genind"
    Error in while (keepCheck) { : missing value where TRUE/FALSE needed
    Calls: loci2genind -> df2genind -> lapply -> FUN -> fillWithZero
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.7
Check: package dependencies
Result: ERROR
    Package required but not available: ‘adegenet’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64-snowleopard