Last updated on 2025-02-21 09:50:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0-4 | 3.32 | 33.77 | 37.09 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.0-4 | 2.64 | 25.36 | 28.00 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0-4 | 59.93 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0-4 | 56.02 | OK | |||
| r-devel-macos-arm64 | 0.0-4 | 24.00 | OK | |||
| r-devel-macos-x86_64 | 0.0-4 | 37.00 | OK | |||
| r-devel-windows-x86_64 | 0.0-4 | 4.00 | 53.00 | 57.00 | OK | |
| r-patched-linux-x86_64 | 0.0-4 | 3.54 | 31.99 | 35.53 | NOTE | |
| r-release-linux-x86_64 | 0.0-4 | 3.19 | 31.95 | 35.14 | NOTE | |
| r-release-macos-arm64 | 0.0-4 | 22.00 | NOTE | |||
| r-release-macos-x86_64 | 0.0-4 | 31.00 | NOTE | |||
| r-release-windows-x86_64 | 0.0-4 | 5.00 | 53.00 | 58.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.0-4 | 22.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.0-4 | 32.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.0-4 | 6.00 | 85.00 | 91.00 | NOTE |
Version: 0.0-4
Check: examples
Result: ERROR
Running examples in ‘ChoR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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: 0x55aec9f80e60>
> # ## 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’
Error in printGraph(NR.gr) : Rgraphviz required for graph printing.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0-4
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64