* using log directory 'd:/RCompile/CRANincoming/R-devel/gapr.Rcheck' * using R Under development (unstable) (2025-05-04 r88189 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'gapr/DESCRIPTION' ... OK * this is package 'gapr' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'ShuYu Lin ' New submission License components with restrictions and base license permitting such: MIT + file LICENSE File 'LICENSE': MIT License Copyright (c) 2025 Shu-Yu Lin Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. The Description field should not start with the package name, 'This package' or similar. * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'gapr' can be installed ... WARNING Found the following significant warnings: hctree_R.cpp:340:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:379:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:380:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:381:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:671:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:672:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:984:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:985:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] hctree_R.cpp:986:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:337:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:339:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:341:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:343:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:402:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:404:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:406:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] r2e_R.cpp:408:20: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] See 'd:/RCompile/CRANincoming/R-devel/gapr.Rcheck/00install.out' for details. * used C++ compiler: 'g++.exe (GCC) 14.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 ... [22s] OK * checking Rd files ... NOTE checkRd: (-1) computeProximity.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeProximity.Rd:46: Lost braces in \itemize; meant \describe ? * 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [13s] ERROR Running examples in 'gapr-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: computeProximity > ### Title: Compute Proximity Matrix > ### Aliases: computeProximity > > ### ** Examples > > # ======================= > # Example 1: Crabs dataset with distance method (Euclidean distance) > # ======================= > # Step 1: Compute proximity matrix > if (requireNamespace("MASS", quietly = TRUE)) { + df_crabs <- as.matrix(MASS::crabs[, -c(1:3)]) # Use continuous variables only + row_prox_crabs <- computeProximity( + data = df_crabs, + proxType = 0, # 0 = Euclidean distance + side = 0, # 0 = row-wise proximity + isContainMissingValue = 0 + ) + + # Step 2: Obtain R2E ordering + r2e_order_crabs <- ellipse_sort(row_prox_crabs) # R2E ordering + + # Step 3: Apply AVG-R2E ordering + hctree_result_crabs <- hctree_sort( + row_prox_crabs, # use distance matrix directly + externalOrder = r2e_order_crabs, # apply r2e order + orderType = 2, # 2 = Average-linkage + flipType = 1 # 1 = Flip based on externalOrder + ) + + avg_r2e_order_crabs <- hctree_result_crabs$order + 1 + + # Inspect results + avg_r2e_order_crabs + } [1] 150 149 50 200 148 145 144 147 146 143 142 199 198 197 195 45 46 49 [19] 48 47 44 100 196 193 192 188 194 189 190 191 187 186 141 140 139 138 [37] 134 135 133 42 43 41 40 37 35 99 98 180 179 185 184 176 183 97 [55] 136 137 132 131 127 130 36 38 39 34 32 31 33 28 177 178 182 181 [73] 172 171 175 174 95 92 96 94 29 30 128 129 126 88 91 83 89 93 [91] 90 87 173 170 169 26 25 24 27 23 22 21 84 86 85 82 168 167 [109] 166 163 164 165 162 125 123 124 161 121 122 120 81 80 79 160 159 78 [127] 118 20 158 157 113 115 112 114 119 117 111 77 76 73 19 75 18 17 [145] 14 13 16 71 74 12 15 11 72 70 116 110 108 156 109 155 107 65 [163] 69 67 68 64 66 10 63 154 9 8 106 153 105 7 62 60 6 51 [181] 1 101 151 152 104 61 59 58 57 56 103 102 5 4 55 54 3 52 [199] 53 2 > > # ======================= > # Example 2: Crabs dataset with distance method (Pearson correlation) > # ======================= > if (requireNamespace("MASS", quietly = TRUE)) { + df_crabs <- as.matrix(MASS::crabs[, -c(1:3)]) # Use continuous variables only + row_prox_pearson <- computeProximity( + data = df_crabs, + proxType = 0, # 0 = Pearson correlation (internally 1 - cor) + side = 0, # 0 = row-wise proximity + isContainMissingValue = 0 + ) + + # Step 2: Obtain R2E ordering + r2e_order_pearson <- ellipse_sort(row_prox_pearson) # R2E ordering + + # Step 3: Inspect results + dist_pearson <- 1 - row_prox_pearson # convert correlation matrix to distance matrix + + hctree_result_pearson <- hctree_sort( + dist_pearson, # use distance matrix directly + externalOrder = r2e_order_pearson, # apply r2e order + orderType = 2, # 2 = Average-linkage + flipType = 1 # 1 = Flip based on externalOrder + ) + + avg_r2e_order_pearson <- hctree_result_pearson$order + 1 + + # Inspect results + avg_r2e_order_pearson + } [1] 84 26 89 25 86 91 93 90 29 88 174 96 30 172 173 128 33 181 [19] 178 36 39 136 177 180 14 38 134 72 191 64 189 9 194 106 46 7 [37] 196 61 151 44 146 4 1 50 150 51 200 101 149 2 183 147 53 145 [55] 3 195 55 144 54 148 52 199 102 48 5 198 103 49 56 143 57 197 [73] 58 47 152 142 59 193 104 100 60 45 6 192 105 188 62 190 153 141 [91] 65 186 8 99 154 35 42 63 187 66 98 107 140 68 43 69 41 67 [109] 139 10 138 155 13 185 109 133 70 97 40 108 176 16 184 12 116 135 [127] 11 37 110 137 15 156 112 179 71 17 75 182 113 132 74 76 131 73 [145] 18 34 115 95 19 32 130 114 158 28 157 94 119 77 127 78 175 117 [163] 31 125 111 92 81 20 164 159 129 120 171 122 161 126 23 118 79 87 [181] 160 170 21 121 80 123 169 22 168 124 83 24 165 163 27 162 82 167 [199] 166 85 > > > > base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") > base::cat("computeProximity", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > ### *