CRAN Package Check Results for Package ChoR

Last updated on 2025-02-23 21:51:05 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	2.57	25.72	28.29	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	3.51	31.26	34.77	NOTE
r-release-linux-x86_64	0.0-4	3.29	31.88	35.17	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	4.00	60.00	64.00	NOTE

Check Details

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: 0x563144db14a0> > # ## 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