* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/DataSimilarity.Rcheck’ * using R Under development (unstable) (2025-12-20 r89211) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘DataSimilarity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DataSimilarity’ version ‘0.2.0’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 whether package ‘DataSimilarity’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [17s/18s] OK * checking Rd files ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [15s/16s] ERROR Running examples in ‘DataSimilarity-Ex.R’ failed The error most likely occurred in: > ### Name: DataSimilarity > ### Title: Dataset Similarity > ### Aliases: DataSimilarity > > ### ** Examples > > # Workflow for using the DataSimilarity package: > # Prepare data example: comparing species in iris dataset > data("iris") > iris.split <- split(iris[, -5], iris$Species) > setosa <- iris.split$setosa > versicolor <- iris.split$versicolor > virginica <- iris.split$virginica > > # 1. Find appropriate methods that can be used to compare 3 numeric datasets: > findSimilarityMethod(Numeric = TRUE, Multiple.Samples = TRUE) [1] "BallDivergence" "C2ST" "DISCOB" "DISCOF" [5] "Energy" "FStest" "KMD" "MMCM" [9] "MW" "Petrie" "RItest" "SC" > > # get more information > findSimilarityMethod(Numeric = TRUE, Multiple.Samples = TRUE, only.names = FALSE) Method Implementation Target.Inclusion 2 Pan et al. (2018) BallDivergence Unfulfilled 7 C2ST (Lopez-Paz and Oquab, 2017) C2ST Unfulfilled 15 DISCO (Rizzo and Székely, 2010) DISCOB Unfulfilled 16 DISCO (Rizzo and Székely, 2010) DISCOF Unfulfilled 18 Energy statistic (Zech and Aslan, 2003) Energy Unfulfilled 22 Paul, De and Ghosh (2022) FStest Unfulfilled 27 KMD (Huang and Sen, 2023) KMD Unfulfilled 29 Mukherjee et al. (2022) MMCM Unfulfilled 31 Mukhopadhyay and Wang (2020) MW Unfulfilled 34 Petrie (2016) Petrie Unfulfilled 35 Paul, De and Ghosh (2022) RItest Unfulfilled 37 Song and Chen (2022) SC Unfulfilled Numeric Categorical Unequal.Sample.Sizes 2 Fulfilled Unfulfilled Fulfilled 7 Fulfilled Conditionally Fulfilled Fulfilled 15 Fulfilled Unfulfilled Fulfilled 16 Fulfilled Unfulfilled Fulfilled 18 Fulfilled Unfulfilled Fulfilled 22 Fulfilled Unfulfilled Fulfilled 27 Fulfilled Unfulfilled Fulfilled 29 Fulfilled Fulfilled Fulfilled 31 Fulfilled Unfulfilled Fulfilled 34 Fulfilled Fulfilled Fulfilled 35 Fulfilled Unfulfilled Fulfilled 37 Fulfilled Unfulfilled Fulfilled p.Larger.N Multiple.Samples Without.training No.assumptions 2 Fulfilled Fulfilled Fulfilled Fulfilled 7 Conditionally Fulfilled Fulfilled Unfulfilled Unfulfilled 15 Fulfilled Fulfilled Fulfilled Unfulfilled 16 Fulfilled Fulfilled Fulfilled Unfulfilled 18 Fulfilled Fulfilled Fulfilled Unfulfilled 22 Fulfilled Fulfilled Fulfilled Fulfilled 27 Fulfilled Fulfilled Fulfilled Fulfilled 29 Fulfilled Fulfilled Fulfilled Unfulfilled 31 Fulfilled Fulfilled Fulfilled Unfulfilled 34 Fulfilled Fulfilled Fulfilled Unfulfilled 35 Fulfilled Fulfilled Fulfilled Fulfilled 37 Fulfilled Fulfilled Fulfilled Unfulfilled No.parameters Implemented Complexity Interpretable.units 2 Unfulfilled Fulfilled Unfulfilled 7 Unfulfilled Fulfilled Fulfilled 15 Unfulfilled Fulfilled O(N^2) Unfulfilled 16 Unfulfilled Fulfilled O(N^2) Unfulfilled 18 Fulfilled Fulfilled O(N^2) Unfulfilled 22 Unfulfilled Fulfilled Unfulfilled 27 Unfulfilled Fulfilled O(KN log N) Unfulfilled 29 Fulfilled Fulfilled Unfulfilled 31 Unfulfilled Fulfilled Unfulfilled 34 Unfulfilled Fulfilled O(N^2 log N),O(N^3),O(N log N) Fulfilled 35 Unfulfilled Fulfilled Unfulfilled 37 Unfulfilled Fulfilled Unfulfilled Lower.bound Upper.bound Rotation.invariant Location.change.invariant 2 0 7 0 1 Conditionally Fulfilled Conditionally Fulfilled 15 0 Unfulfilled Fulfilled Fulfilled 16 0 Unfulfilled Fulfilled Fulfilled 18 0 Unfulfilled Fulfilled Fulfilled 22 0 1 Conditionally Fulfilled Conditionally Fulfilled 27 0 1 Fulfilled Fulfilled 29 0 Fulfilled Fulfilled 31 0 34 Fulfilled Fulfilled Fulfilled Fulfilled 35 0 1 Conditionally Fulfilled Conditionally Fulfilled 37 0 Fulfilled Fulfilled Homogeneous.scale.invariant Positive.definite Symmetric Triangle.inequality 2 Fulfilled Fulfilled Unfulfilled 7 Conditionally Fulfilled Fulfilled 15 Unfulfilled Fulfilled 16 Unfulfilled Fulfilled 18 Unfulfilled Fulfilled Fulfilled Fulfilled 22 Fulfilled 27 Fulfilled Fulfilled Fulfilled 29 Fulfilled Fulfilled 31 Fulfilled 34 Fulfilled Fulfilled 35 Fulfilled 37 Fulfilled Fulfilled Consistency.N Consistency.p Number.Fulfilled 2 Fulfilled 11 7 Conditionally Fulfilled 7 15 Fulfilled 11 16 Fulfilled 11 18 Fulfilled Conditionally Fulfilled 14 22 Fulfilled 11 27 Fulfilled 16 29 Fulfilled 14 31 9 34 13 35 Fulfilled 11 37 Fulfilled 12 Number.Cond.Fulfilled Number.Unfulfilled Number.NA 2 0 5 5 7 6 5 3 15 0 7 3 16 0 7 3 18 1 6 0 22 3 3 4 27 0 3 2 29 0 3 4 31 0 4 8 34 0 4 4 35 3 3 4 37 0 5 4 Class 2 Testing approach 7 Method based on binary classification 15 Comparison based on inter-point distances 16 Comparison based on inter-point distances 18 Comparison based on inter-point distances 22 Testing approach 27 Kernel-based 29 Graph-based 31 Graph-based 34 Graph-based 35 Testing approach 37 Graph-based Subclass 2 Testing approach 7 Method based on binary classification 15 Comparison based on inter-point distances 16 Comparison based on inter-point distances 18 Comparison based on inter-point distances 22 Testing approach 27 Kernel-based 29 Graph-based 31 Graph-based 34 Graph-based 35 Testing approach 37 Graph-based > > # 2. Choose a method and apply it: > # All suitable methods > possible.methds <- findSimilarityMethod(Numeric = TRUE, Multiple.Samples = TRUE, + only.names = FALSE) > # Select, e.g., method with highest number of fulfilled criteria > possible.methds$Implementation[which.max(possible.methds$Number.Fulfilled)] [1] "KMD" > > set.seed(1234) > if(requireNamespace("KMD")) { + DataSimilarity(setosa, versicolor, virginica, method = "KMD") + } Loading required namespace: KMD Error in `[.data.table`(df_X, , `:=`(gp_size, length(id)), by = "group") : attempt access index 2/2 in VECTOR_ELT Calls: DataSimilarity ... -> -> get_neighbors -> [ -> [.data.table Execution halted * checking examples with --run-donttest ... [14s/14s] ERROR Running examples in ‘DataSimilarity-Ex.R’ failed The error most likely occurred in: > ### Name: DataSimilarity > ### Title: Dataset Similarity > ### Aliases: DataSimilarity > > ### ** Examples > > # Workflow for using the DataSimilarity package: > # Prepare data example: comparing species in iris dataset > data("iris") > iris.split <- split(iris[, -5], iris$Species) > setosa <- iris.split$setosa > versicolor <- iris.split$versicolor > virginica <- iris.split$virginica > > # 1. Find appropriate methods that can be used to compare 3 numeric datasets: > findSimilarityMethod(Numeric = TRUE, Multiple.Samples = TRUE) [1] "BallDivergence" "C2ST" "DISCOB" "DISCOF" [5] "Energy" "FStest" "KMD" "MMCM" [9] "MW" "Petrie" "RItest" "SC" > > # get more information > findSimilarityMethod(Numeric = TRUE, Multiple.Samples = TRUE, only.names = FALSE) Method Implementation Target.Inclusion 2 Pan et al. (2018) BallDivergence Unfulfilled 7 C2ST (Lopez-Paz and Oquab, 2017) C2ST Unfulfilled 15 DISCO (Rizzo and Székely, 2010) DISCOB Unfulfilled 16 DISCO (Rizzo and Székely, 2010) DISCOF Unfulfilled 18 Energy statistic (Zech and Aslan, 2003) Energy Unfulfilled 22 Paul, De and Ghosh (2022) FStest Unfulfilled 27 KMD (Huang and Sen, 2023) KMD Unfulfilled 29 Mukherjee et al. (2022) MMCM Unfulfilled 31 Mukhopadhyay and Wang (2020) MW Unfulfilled 34 Petrie (2016) Petrie Unfulfilled 35 Paul, De and Ghosh (2022) RItest Unfulfilled 37 Song and Chen (2022) SC Unfulfilled Numeric Categorical Unequal.Sample.Sizes 2 Fulfilled Unfulfilled Fulfilled 7 Fulfilled Conditionally Fulfilled Fulfilled 15 Fulfilled Unfulfilled Fulfilled 16 Fulfilled Unfulfilled Fulfilled 18 Fulfilled Unfulfilled Fulfilled 22 Fulfilled Unfulfilled Fulfilled 27 Fulfilled Unfulfilled Fulfilled 29 Fulfilled Fulfilled Fulfilled 31 Fulfilled Unfulfilled Fulfilled 34 Fulfilled Fulfilled Fulfilled 35 Fulfilled Unfulfilled Fulfilled 37 Fulfilled Unfulfilled Fulfilled p.Larger.N Multiple.Samples Without.training No.assumptions 2 Fulfilled Fulfilled Fulfilled Fulfilled 7 Conditionally Fulfilled Fulfilled Unfulfilled Unfulfilled 15 Fulfilled Fulfilled Fulfilled Unfulfilled 16 Fulfilled Fulfilled Fulfilled Unfulfilled 18 Fulfilled Fulfilled Fulfilled Unfulfilled 22 Fulfilled Fulfilled Fulfilled Fulfilled 27 Fulfilled Fulfilled Fulfilled Fulfilled 29 Fulfilled Fulfilled Fulfilled Unfulfilled 31 Fulfilled Fulfilled Fulfilled Unfulfilled 34 Fulfilled Fulfilled Fulfilled Unfulfilled 35 Fulfilled Fulfilled Fulfilled Fulfilled 37 Fulfilled Fulfilled Fulfilled Unfulfilled No.parameters Implemented Complexity Interpretable.units 2 Unfulfilled Fulfilled Unfulfilled 7 Unfulfilled Fulfilled Fulfilled 15 Unfulfilled Fulfilled O(N^2) Unfulfilled 16 Unfulfilled Fulfilled O(N^2) Unfulfilled 18 Fulfilled Fulfilled O(N^2) Unfulfilled 22 Unfulfilled Fulfilled Unfulfilled 27 Unfulfilled Fulfilled O(KN log N) Unfulfilled 29 Fulfilled Fulfilled Unfulfilled 31 Unfulfilled Fulfilled Unfulfilled 34 Unfulfilled Fulfilled O(N^2 log N),O(N^3),O(N log N) Fulfilled 35 Unfulfilled Fulfilled Unfulfilled 37 Unfulfilled Fulfilled Unfulfilled Lower.bound Upper.bound Rotation.invariant Location.change.invariant 2 0 7 0 1 Conditionally Fulfilled Conditionally Fulfilled 15 0 Unfulfilled Fulfilled Fulfilled 16 0 Unfulfilled Fulfilled Fulfilled 18 0 Unfulfilled Fulfilled Fulfilled 22 0 1 Conditionally Fulfilled Conditionally Fulfilled 27 0 1 Fulfilled Fulfilled 29 0 Fulfilled Fulfilled 31 0 34 Fulfilled Fulfilled Fulfilled Fulfilled 35 0 1 Conditionally Fulfilled Conditionally Fulfilled 37 0 Fulfilled Fulfilled Homogeneous.scale.invariant Positive.definite Symmetric Triangle.inequality 2 Fulfilled Fulfilled Unfulfilled 7 Conditionally Fulfilled Fulfilled 15 Unfulfilled Fulfilled 16 Unfulfilled Fulfilled 18 Unfulfilled Fulfilled Fulfilled Fulfilled 22 Fulfilled 27 Fulfilled Fulfilled Fulfilled 29 Fulfilled Fulfilled 31 Fulfilled 34 Fulfilled Fulfilled 35 Fulfilled 37 Fulfilled Fulfilled Consistency.N Consistency.p Number.Fulfilled 2 Fulfilled 11 7 Conditionally Fulfilled 7 15 Fulfilled 11 16 Fulfilled 11 18 Fulfilled Conditionally Fulfilled 14 22 Fulfilled 11 27 Fulfilled 16 29 Fulfilled 14 31 9 34 13 35 Fulfilled 11 37 Fulfilled 12 Number.Cond.Fulfilled Number.Unfulfilled Number.NA 2 0 5 5 7 6 5 3 15 0 7 3 16 0 7 3 18 1 6 0 22 3 3 4 27 0 3 2 29 0 3 4 31 0 4 8 34 0 4 4 35 3 3 4 37 0 5 4 Class 2 Testing approach 7 Method based on binary classification 15 Comparison based on inter-point distances 16 Comparison based on inter-point distances 18 Comparison based on inter-point distances 22 Testing approach 27 Kernel-based 29 Graph-based 31 Graph-based 34 Graph-based 35 Testing approach 37 Graph-based Subclass 2 Testing approach 7 Method based on binary classification 15 Comparison based on inter-point distances 16 Comparison based on inter-point distances 18 Comparison based on inter-point distances 22 Testing approach 27 Kernel-based 29 Graph-based 31 Graph-based 34 Graph-based 35 Testing approach 37 Graph-based > > # 2. Choose a method and apply it: > # All suitable methods > possible.methds <- findSimilarityMethod(Numeric = TRUE, Multiple.Samples = TRUE, + only.names = FALSE) > # Select, e.g., method with highest number of fulfilled criteria > possible.methds$Implementation[which.max(possible.methds$Number.Fulfilled)] [1] "KMD" > > set.seed(1234) > if(requireNamespace("KMD")) { + DataSimilarity(setosa, versicolor, virginica, method = "KMD") + } Loading required namespace: KMD Error in `[.data.table`(df_X, , `:=`(gp_size, length(id)), by = "group") : attempt access index 2/2 in VECTOR_ELT Calls: DataSimilarity ... -> -> get_neighbors -> [ -> [.data.table Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [240s/236s] [241s/237s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [320s/324s] OK * checking PDF version of manual ... [12s/12s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs See ‘/data/blackswan/ripley/R/packages/tests-devel/DataSimilarity.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 11:27.73, 649.30 + 34.83