CRAN Package Check Results for Package ChoR

Last updated on 2020-03-27 00:49:17 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0-4 3.99 38.99 42.98 OK
r-devel-linux-x86_64-debian-gcc 0.0-4 2.92 29.76 32.68 OK
r-devel-linux-x86_64-fedora-clang 0.0-4 48.68 OK
r-devel-linux-x86_64-fedora-gcc 0.0-4 50.05 OK
r-devel-windows-ix86+x86_64 0.0-4 10.00 48.00 58.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 0.0-4 8.00 52.00 60.00 OK
r-patched-linux-x86_64 0.0-4 3.18 34.52 37.70 OK
r-release-linux-x86_64 0.0-4 3.21 35.04 38.25 OK
r-release-windows-ix86+x86_64 0.0-4 12.00 61.00 73.00 OK
r-release-osx-x86_64 0.0-4 NOTE
r-oldrel-windows-ix86+x86_64 0.0-4 8.00 61.00 69.00 OK
r-oldrel-osx-x86_64 0.0-4 OK

Check Details

Version: 0.0-4
Check: examples
Result: ERROR
    Running examples in 'ChoR-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: ChoR
    > ### Title: Getting started with the ChoR package
    > ### Aliases: ChoR ChoR-package
    > ### Keywords: linear-log-analysis model package
    >
    > ### ** Examples
    >
    > # Warning: RJava requires to **copy** your data from R into a JVM.
    > # If you need extra memory, use this option (here, for 4Gb) **before** loading choR.
    > # Note: not needed in our case, kept for the example
    > options( java.parameters = "-Xmx4g" )
    > library(ChoR)
    >
    > # Helper function for graph printing. Require Rgraphviz:
    > # source("https://bioconductor.org/biocLite.R")
    > # biocLite("Rgraphviz")
    > printGraph = function(x){
    + if(requireNamespace("Rgraphviz", quietly=TRUE)){
    + attrs <- list(node=list(shape="ellipse", fixedsize=FALSE, fontsize=25))
    + Rgraphviz::plot(x, attrs=attrs)
    + } else { stop("Rgraphviz required for graph printing.") }
    + }
    >
    >
    > ###### MUSHROOM #####
    > # We are using a partial UCI mushroom data set (the example should not be too long)
    > MR.url = system.file("extdata", "mushrooms.csv", package = "ChoR", mustWork = TRUE)
    >
    > MR.data =
    + read.csv(
    + MR.url,
    + header = TRUE, # Here, we have a header
    + na.strings = c("NA","?",""), # Configure the missing values
    + stringsAsFactors = FALSE, # Keep strings for now
    + check.names = TRUE # Replace some special characters
    + )
    >
    > # This file has a special line with types. You can check this with MR.data[1,].
    > # Let's remove it:
    > MR.data = MR.data[-1, ]
    >
    > # Launch the SMT analysis, with:
    > # ## default pValueThreshold=0.05
    > # ## computation of attributes cardinality from the data
    > MR.res = ChoR.SMT(MR.data)
    >
    > # Access the result:
    > # ## As a list of cliques:
    > NR.cl = ChoR.as.cliques(MR.res)
    > print(NR.cl)
    [[1]]
    [1] "type" "cap_shape" "bruises" "stalk_shape" "stalk_root"
    
    [[2]]
    [1] "type" "bruises" "stalk_shape" "stalk_root" "population"
    
    [[3]]
    [1] "cap_color" "bruises" "stalk_shape" "stalk_root" "population"
    
    [[4]]
    [1] "cap_color" "bruises" "gill_spacing" "stalk_shape" "population"
    
    [[5]]
    [1] "cap_surface" "bruises" "gill_spacing" "stalk_shape" "population"
    
    [[6]]
    [1] "cap_surface" "bruises"
    [3] "gill_spacing" "stalk_surface_below_ring"
    [5] "population"
    
    [[7]]
    [1] "type" "bruises" "stalk_shape" "stalk_root" "habitat"
    
    [[8]]
    [1] "type" "bruises" "odor" "stalk_shape"
    
    [[9]]
    [1] "type" "gill_size" "stalk_shape" "stalk_root"
    
    [[10]]
    [1] "bruises" "gill_color" "stalk_shape" "stalk_root"
    
    [[11]]
    [1] "type" "gill_size" "stalk_shape"
    [4] "spore_print_color"
    
    [[12]]
    [1] "bruises" "gill_spacing"
    [3] "stalk_surface_above_ring"
    
    [[13]]
    [1] "gill_spacing" "stalk_shape" "stalk_color_above_ring"
    
    [[14]]
    [1] "gill_spacing" "stalk_shape" "stalk_color_below_ring"
    
    [[15]]
    [1] "bruises" "gill_spacing" "ring_type"
    
    [[16]]
    [1] "gill_attachment"
    
    [[17]]
    [1] "veil_type"
    
    [[18]]
    [1] "veil_color"
    
    [[19]]
    [1] "ring_number"
    
    > # ## As a formula
    > NR.fo = ChoR.as.formula(MR.res)
    > print(NR.fo)
    ~type * cap_shape * bruises * stalk_shape * stalk_root + type *
     bruises * stalk_shape * stalk_root * population + cap_color *
     bruises * stalk_shape * stalk_root * population + cap_color *
     bruises * gill_spacing * stalk_shape * population + cap_surface *
     bruises * gill_spacing * stalk_shape * population + cap_surface *
     bruises * gill_spacing * stalk_surface_below_ring * population +
     type * bruises * stalk_shape * stalk_root * habitat + type *
     bruises * odor * stalk_shape + type * gill_size * stalk_shape *
     stalk_root + bruises * gill_color * stalk_shape * stalk_root +
     type * gill_size * stalk_shape * spore_print_color + bruises *
     gill_spacing * stalk_surface_above_ring + gill_spacing *
     stalk_shape * stalk_color_above_ring + gill_spacing * stalk_shape *
     stalk_color_below_ring + bruises * gill_spacing * ring_type +
     gill_attachment + veil_type + veil_color + ring_number
    <environment: 0x0000000009379440>
    > # ## As a graph
    > if(requireNamespace("graph", quietly=TRUE)){
    + NR.gr = ChoR.as.graph(MR.res)
    + printGraph(NR.gr)
    + } else {
    + print("'graph' package not installed; Skipping 'as graph' example.")
    + }
    Warning in .local(from, to, graph) : edges replaced: 'type|bruises'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_shape'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_root|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'cap_color|bruises'
    Warning in .local(from, to, graph) :
     edges replaced: 'cap_color|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'cap_color|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|gill_spacing'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'gill_spacing|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'gill_spacing|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'cap_surface|bruises'
    Warning in .local(from, to, graph) :
     edges replaced: 'cap_surface|gill_spacing'
    Warning in .local(from, to, graph) :
     edges replaced: 'cap_surface|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|gill_spacing'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|population'
    Warning in .local(from, to, graph) :
     edges replaced: 'gill_spacing|population'
    Warning in .local(from, to, graph) : edges replaced: 'type|bruises'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_shape'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|stalk_root'
    Warning in .local(from, to, graph) : edges replaced: 'type|bruises'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_shape'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|stalk_root'
    Warning in .local(from, to, graph) :
     edges replaced: 'stalk_shape|stalk_root'
    Warning in .local(from, to, graph) : edges replaced: 'type|gill_size'
    Warning in .local(from, to, graph) : edges replaced: 'type|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'gill_size|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|gill_spacing'
    Warning in .local(from, to, graph) :
     edges replaced: 'gill_spacing|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'gill_spacing|stalk_shape'
    Warning in .local(from, to, graph) :
     edges replaced: 'bruises|gill_spacing'
    Warning: multiple methods tables found for 'plot'
    Error in as.double(y) :
     cannot coerce type 'S4' to vector of type 'double'
    Calls: printGraph ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.0-4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Flavor: r-release-osx-x86_64