• using R Under development (unstable) (2025-02-20 r87772)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-16) 14.2.0     GNU Fortran (Debian 14.2.0-16) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘ChoR/DESCRIPTION’ ... OK
• this is package ‘ChoR’ version ‘0.0-4’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘Rgraphviz’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘ChoR’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [1s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [4s/6s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking LazyData ... INFO   'LazyData' is specified without a 'data' directory
• checking line endings in Makefiles ... OK
• checking for GNU extensions in Makefiles ... OK
• checking include directives in Makefiles ... OK
• checking examples ... [2s/2s] 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: 0x56021969ede0> > # ## 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
• checking PDF version of manual ... [3s/5s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR