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 read the data from internet: http://repository.seasr.org/Datasets/UCI/csv/mushroom.csv
> MR.data =
+   read.csv(  "http://repository.seasr.org/Datasets/UCI/csv/mushroom.csv",
+               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)
Warning in ChoR.loadData(x, card) :
  missing values in 'x', treated as a possible value.
> 
> # Access the result:
> # ## As a list of cliques:
> NR.cl = ChoR.as.cliques(MR.res)
> print(NR.cl)
[[1]]
[1] "cap.shape"   "bruises."    "gill.size"   "stalk.shape" "ring.number"
[6] "class"      

[[2]]
[1] "cap.color"    "bruises."     "gill.spacing" "gill.size"    "stalk.shape" 
[6] "ring.number"  "class"       

[[3]]
[1] "bruises."        "gill.attachment" "gill.spacing"    "gill.size"      
[5] "stalk.shape"     "ring.number"     "class"          

[[4]]
[1] "bruises."     "gill.spacing" "gill.size"    "stalk.shape"  "stalk.root"  
[6] "ring.number"  "class"       

[[5]]
[1] "cap.surface"  "bruises."     "gill.spacing" "gill.size"    "stalk.shape" 
[6] "stalk.root"   "class"       

[[6]]
[1] "bruises."                 "gill.attachment"         
[3] "gill.size"                "stalk.shape"             
[5] "stalk.surface.below.ring" "ring.number"             
[7] "class"                   

[[7]]
[1] "bruises."               "gill.spacing"           "gill.size"             
[4] "stalk.shape"            "stalk.color.below.ring" "ring.number"           
[7] "class"                 

[[8]]
[1] "bruises."     "gill.spacing" "gill.size"    "stalk.shape"  "ring.number" 
[6] "ring.type"    "class"       

[[9]]
[1] "bruises."          "gill.spacing"      "gill.size"        
[4] "stalk.shape"       "ring.number"       "spore.print.color"
[7] "class"            

[[10]]
[1] "gill.attachment" "gill.spacing"    "gill.size"       "stalk.shape"    
[5] "ring.number"     "population"      "class"          

[[11]]
[1] "bruises."     "gill.spacing" "gill.size"    "stalk.shape"  "ring.number" 
[6] "habitat"      "class"       

[[12]]
[1] "bruises."    "odor"        "gill.size"   "stalk.shape" "ring.number"
[6] "class"      

[[13]]
[1] "bruises."        "gill.attachment" "gill.size"       "gill.color"     
[5] "stalk.shape"     "class"          

[[14]]
[1] "bruises."                 "gill.spacing"            
[3] "gill.size"                "stalk.shape"             
[5] "stalk.surface.above.ring" "class"                   

[[15]]
[1] "bruises."               "gill.attachment"        "gill.size"             
[4] "stalk.shape"            "stalk.color.above.ring" "class"                 

[[16]]
[1] "gill.attachment" "gill.spacing"    "veil.color"      "class"          

[[17]]
[1] "veil.type"

> # ## As a formula
> NR.fo = ChoR.as.formula(MR.res)
> print(NR.fo)
~cap.shape * bruises. * gill.size * stalk.shape * ring.number * 
    class + cap.color * bruises. * gill.spacing * gill.size * 
    stalk.shape * ring.number * class + bruises. * gill.attachment * 
    gill.spacing * gill.size * stalk.shape * ring.number * class + 
    bruises. * gill.spacing * gill.size * stalk.shape * stalk.root * 
        ring.number * class + cap.surface * bruises. * gill.spacing * 
    gill.size * stalk.shape * stalk.root * class + bruises. * 
    gill.attachment * gill.size * stalk.shape * stalk.surface.below.ring * 
    ring.number * class + bruises. * gill.spacing * gill.size * 
    stalk.shape * stalk.color.below.ring * ring.number * class + 
    bruises. * gill.spacing * gill.size * stalk.shape * ring.number * 
        ring.type * class + bruises. * gill.spacing * gill.size * 
    stalk.shape * ring.number * spore.print.color * class + gill.attachment * 
    gill.spacing * gill.size * stalk.shape * ring.number * population * 
    class + bruises. * gill.spacing * gill.size * stalk.shape * 
    ring.number * habitat * class + bruises. * odor * gill.size * 
    stalk.shape * ring.number * class + bruises. * gill.attachment * 
    gill.size * gill.color * stalk.shape * class + bruises. * 
    gill.spacing * gill.size * stalk.shape * stalk.surface.above.ring * 
    class + bruises. * gill.attachment * gill.size * stalk.shape * 
    stalk.color.above.ring * class + gill.attachment * gill.spacing * 
    veil.color * class + veil.type
<environment: 0x3a1f218>
> # ## As a graph
> NR.gr = ChoR.as.graph(MR.res)
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
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.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.root’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.root’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|stalk.root’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) : edges replaced: ‘stalk.root|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.attachment’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|ring.number’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|ring.number’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘ring.number|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.attachment’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.attachment’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘bruises.|stalk.shape’
Warning in .local(from, to, graph) : edges replaced: ‘bruises.|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|gill.size’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|stalk.shape’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.size|stalk.shape’
Warning in .local(from, to, graph) : edges replaced: ‘gill.size|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘stalk.shape|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|gill.spacing’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.attachment|class’
Warning in .local(from, to, graph) :
  edges replaced: ‘gill.spacing|class’
> printGraph(NR.gr)
> 
> 
> 
> ###### Solar flare #####
> SF.data =
+   read.csv( "https://archive.ics.uci.edu/ml/machine-learning-databases/solar-flare/flare.data2",
+             sep               = "",       # White spaces
+             skip              = 1,
+             header            = FALSE,
+             stringsAsFactors  = FALSE,
+             check.names       = TRUE
+           )
Warning in file(file, "rt") :
  URL 'https://archive.ics.uci.edu/ml/machine-learning-databases/solar-flare/flare.data2': status was 'Couldn't connect to server'
Error in file(file, "rt") : 
  cannot open the connection to 'https://archive.ics.uci.edu/ml/machine-learning-databases/solar-flare/flare.data2'
Calls: read.csv -> read.table -> file
Execution halted