CRAN Package Check Results for Package pegas

Last updated on 2021-05-06 23:49:40 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 30.37 246.81 277.18 OK
r-devel-linux-x86_64-debian-gcc 1.0 25.56 183.97 209.53 OK
r-devel-linux-x86_64-fedora-clang 1.0 339.52 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 328.33 OK
r-devel-windows-ix86+x86_64 1.0 47.00 380.00 427.00 OK
r-devel-windows-x86_64-gcc10-UCRT 1.0 OK
r-patched-linux-x86_64 1.0 32.64 235.83 268.47 OK
r-patched-solaris-x86 1.0 471.90 OK
r-release-linux-x86_64 1.0 27.86 226.25 254.11 OK
r-release-macos-x86_64 1.0 OK
r-release-windows-ix86+x86_64 1.0 48.00 282.00 330.00 OK
r-oldrel-macos-x86_64 1.0 ERROR
r-oldrel-windows-ix86+x86_64 1.0 56.00 233.00 289.00 ERROR

Check Details

Version: 1.0
Check: Rd cross-references
Result: NOTE
    Undeclared packages ‘ade4’, ‘vegan’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘pegas-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cophenetic.haploNet
    > ### Title: Cophenetic Matrix on Haplotype Networks
    > ### Aliases: cophenetic.haploNet
    > ### Keywords: manip
    >
    > ### ** Examples
    >
    > example(mst)
    
    mst> data(woodmouse)
    
    mst> d <- dist.dna(woodmouse, "n")
    
    mst> (r <- mst(d))
    Haplotype network with:
     15 haplotypes
     14 links
     link lengths between 2 and 14 steps
    
    Use print.default() to display all elements.
    
    mst> plot(r)
    
    mst> ## a case where the RMST and the MJN are identical:
    mst> x <- c(">A", "TAAGTGCAT", ">B", "TAAATGCAT", ">C", "TAGGTGCAT", ">D", "TAAGTACAT",
    mst+ ">E", "TAAGTGTAT", ">F", "TAAGTACAC", ">G", "TAAGTACGT", ">H", "CAAGTACAC",
    mst+ ">I", "CAAGCACAC", ">J", "CAAGTACAT", ">K", "CGAGTACAT", ">L", "TAAGTACGC",
    mst+ ">M", "CAAGCACAT")
    
    mst> fl <- tempfile()
    
    mst> cat(x, file = fl, sep = "\n")
    
    mst> x <- read.dna(fl, "f")
    
    mst> tr <- rmst(dist.dna(x, "n"))
    
    Iteration: 1 Number of links: 12
    Iteration: 2 Number of links: 15
    Iteration: 3 Number of links: 15
    Iteration: 4 Number of links: 15
    Iteration: 5 Number of links: 15
    Iteration: 6 Number of links: 15
    
    mst> ts <- mjn(x)
    Adding median vectors:Error in class(res) <- clx :
     invalid to set the class to matrix unless the dimension attribute is of length 2 (was 0)
    Calls: example ... withVisible -> eval -> eval -> mjn -> funVariableCol -> latag2n
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.0
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'pegas-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: cophenetic.haploNet
    > ### Title: Cophenetic Matrix on Haplotype Networks
    > ### Aliases: cophenetic.haploNet
    > ### Keywords: manip
    >
    > ### ** Examples
    >
    > example(mst)
    
    mst> data(woodmouse)
    
    mst> d <- dist.dna(woodmouse, "n")
    
    mst> (r <- mst(d))
    Haplotype network with:
     15 haplotypes
     14 links
     link lengths between 2 and 14 steps
    
    Use print.default() to display all elements.
    
    mst> plot(r)
    
    mst> ## a case where the RMST and the MJN are identical:
    mst> x <- c(">A", "TAAGTGCAT", ">B", "TAAATGCAT", ">C", "TAGGTGCAT", ">D", "TAAGTACAT",
    mst+ ">E", "TAAGTGTAT", ">F", "TAAGTACAC", ">G", "TAAGTACGT", ">H", "CAAGTACAC",
    mst+ ">I", "CAAGCACAC", ">J", "CAAGTACAT", ">K", "CGAGTACAT", ">L", "TAAGTACGC",
    mst+ ">M", "CAAGCACAT")
    
    mst> fl <- tempfile()
    
    mst> cat(x, file = fl, sep = "\n")
    
    mst> x <- read.dna(fl, "f")
    
    mst> tr <- rmst(dist.dna(x, "n"))
    
    Iteration: 1 Number of links: 12
    Iteration: 2 Number of links: 15
    Iteration: 3 Number of links: 15
    Iteration: 4 Number of links: 15
    Iteration: 5 Number of links: 15
    Iteration: 6 Number of links: 15
    
    mst> ts <- mjn(x)
    Adding median vectors:Error in class(res) <- clx :
     invalid to set the class to matrix unless the dimension attribute is of length 2 (was 0)
    Calls: example ... withVisible -> eval -> eval -> mjn -> funVariableCol -> latag2n
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.0
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'pegas-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: cophenetic.haploNet
    > ### Title: Cophenetic Matrix on Haplotype Networks
    > ### Aliases: cophenetic.haploNet
    > ### Keywords: manip
    >
    > ### ** Examples
    >
    > example(mst)
    
    mst> data(woodmouse)
    
    mst> d <- dist.dna(woodmouse, "n")
    
    mst> (r <- mst(d))
    Haplotype network with:
     15 haplotypes
     14 links
     link lengths between 2 and 14 steps
    
    Use print.default() to display all elements.
    
    mst> plot(r)
    
    mst> ## a case where the RMST and the MJN are identical:
    mst> x <- c(">A", "TAAGTGCAT", ">B", "TAAATGCAT", ">C", "TAGGTGCAT", ">D", "TAAGTACAT",
    mst+ ">E", "TAAGTGTAT", ">F", "TAAGTACAC", ">G", "TAAGTACGT", ">H", "CAAGTACAC",
    mst+ ">I", "CAAGCACAC", ">J", "CAAGTACAT", ">K", "CGAGTACAT", ">L", "TAAGTACGC",
    mst+ ">M", "CAAGCACAT")
    
    mst> fl <- tempfile()
    
    mst> cat(x, file = fl, sep = "\n")
    
    mst> x <- read.dna(fl, "f")
    
    mst> tr <- rmst(dist.dna(x, "n"))
    
    Iteration: 1 Number of links: 12
    Iteration: 2 Number of links: 15
    Iteration: 3 Number of links: 15
    Iteration: 4 Number of links: 15
    Iteration: 5 Number of links: 15
    Iteration: 6 Number of links: 15
    
    mst> ts <- mjn(x)
    Adding median vectors:Error in class(res) <- clx :
     invalid to set the class to matrix unless the dimension attribute is of length 2 (was 0)
    Calls: example ... withVisible -> eval -> eval -> mjn -> funVariableCol -> latag2n
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64