* using log directory 'd:/RCompile/CRANincoming/R-devel/combiroc.Rcheck' * using R Under development (unstable) (2023-07-02 r84627 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'combiroc/DESCRIPTION' ... OK * this is package 'combiroc' version '0.3.3' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [56s] NOTE Maintainer: 'Riccardo L. Rossi ' Possibly misspelled words in DESCRIPTION: bioRxiv (27:554) pre (27:562) Found the following (possibly) invalid URLs: URL: http://combiroc.eu/ From: README.md Status: Error Message: Empty reply from server * 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 whether package 'combiroc' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 R 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 ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'combiroc-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: markers_distribution > ### Title: Show distribution of intensity values for all the markers both > ### singularly and all together. > ### Aliases: markers_distribution > > ### ** Examples > > demo_data # combiroc built-in demo data (proteomics data from Zingaretti et al. 2012 - PMC3518104) Patient.ID Class Marker1 Marker2 Marker3 Marker4 Marker5 1 AIH1 A 438 187 197 298 139 2 AIH2 A 345 293 134 523 335 3 AIH3 A 903 392 300 1253 0 4 AIH4 A 552 267 296 666 22 5 AIH5 A 1451 760 498 884 684 6 AIH6 A 497 260 175 640 572 7 AIH7 A 3878 2858 510 1518 348 8 AIH8 A 740 368 266 1391 647 9 AIH9 A 538 412 282 1071 474 10 AIH10 A 1194 1065 442 1530 816 11 AIH11 A 988 817 394 1626 1028 12 AIH12 A 261 153 528 449 237 13 AIH13 A 312 181 58 408 661 14 AIH14 A 499 302 181 1088 568 15 AIH15 A 998 431 75 397 519 16 AIH16 A 6485 3704 8834 2595 1570 17 AIH17 A 8584 2662 13178 3390 2757 18 AIH18 A 1696 1029 369 468 2422 19 AIH19 A 774 505 251 1014 517 20 AIH20 A 433 330 92 1266 743 21 AIH21 A 1207 1501 57 1847 741 22 AIH22 A 225 849 125 330 168 23 AIH23 A 1327 485 366 563 878 24 AIH24 A 76 582 601 115 73 25 AIH25 A 586 256 53 710 74 26 AIH26 A 263 196 124 798 95 27 AIH27 A 146 568 64 125 92 28 AIH28 A 537 620 82 350 53 29 AIH29 A 52 41 588 346 50 30 AIH30 A 882 138 47 601 85 31 AIH31 A 462 304 81 378 208 32 AIH32 A 372 149 0 460 156 33 AIH33 A 1964 875 404 1883 1021 34 AIH34 A 2809 1633 451 1042 608 35 AIH35 A 994 505 303 1699 783 36 AIH36 A 361 185 115 466 520 37 AIH37 A 275 384 45 329 466 38 AIH38 A 947 622 16 236 728 39 AIH39 A 405 133 32 284 358 40 AIH40 A 922 689 68 105 643 41 no AIH1 B 510 28 0 332 0 42 no AIH2 B 205 0 0 332 0 43 no AIH3 B 44 0 0 332 21 44 no AIH4 B 49 38 7 178 48 45 no AIH5 B 26 33 6 131 32 46 no AIH6 B 24 26 8 206 28 47 no AIH7 B 243 373 109 631 477 48 no AIH8 B 99 111 51 193 197 49 no AIH9 B 85 55 71 811 321 50 no AIH10 B 146 108 46 173 171 51 no AIH11 B 0 113 0 0 56 52 no AIH12 B 151 0 0 360 0 53 no AIH13 B 0 0 0 15 21 54 no AIH14 B 0 5 0 147 53 55 no AIH15 B 118 69 13 748 97 56 no AIH16 B 31 29 7 223 34 57 no AIH17 B 72 53 12 376 85 58 no AIH18 B 137 151 20 662 131 59 no AIH19 B 78 58 6 368 49 60 no AIH20 B 193 14 90 703 177 61 no AIH21 B 0 0 0 0 0 62 no AIH22 B 0 20 0 66 31 63 no AIH23 B 351 70 0 478 7 64 no AIH24 B 171 127 74 1202 224 65 no AIH25 B 77 75 26 316 61 66 no AIH26 B 51 45 2 286 44 67 no AIH27 B 64 55 17 333 46 68 no AIH28 B 150 185 42 975 252 69 no AIH29 B 149 140 52 1087 209 70 no AIH30 B 147 103 19 794 98 71 no AIH31 B 86 89 44 427 144 72 no AIH32 B 94 57 18 581 88 73 no AIH33 B 56 41 23 244 49 74 no AIH34 B 10 15 2 121 26 75 no AIH35 B 46 22 0 69 24 76 no AIH36 B 84 65 4 278 77 77 no AIH37 B 42 44 19 306 86 78 no AIH38 B 46 51 24 342 74 79 no AIH39 B 73 39 9 358 41 80 no AIH40 B 83 131 27 1012 124 81 no AIH41 B 0 193 50 382 135 82 no AIH42 B 41 94 64 464 141 83 no AIH43 B 0 77 46 398 85 84 no AIH44 B 98 152 91 469 301 85 no AIH45 B 78 85 10 407 0 86 no AIH46 B 21 16 0 536 16 87 no AIH47 B 44 34 74 266 21 88 no AIH48 B 144 76 63 252 0 89 no AIH49 B 162 249 101 134 0 90 no AIH50 B 100 169 33 1430 0 91 no AIH51 B 52 159 57 681 417 92 no AIH52 B 97 86 64 591 33 93 no AIH53 B 73 80 20 157 51 94 no AIH54 B 162 117 25 749 0 95 no AIH55 B 100 220 37 729 41 96 no AIH56 B 227 174 26 290 0 97 no AIH57 B 136 165 23 315 40 98 no AIH58 B 96 213 47 682 780 99 no AIH59 B 69 59 21 629 245 100 no AIH60 B 74 70 67 138 215 101 no AIH61 B 129 118 44 117 769 102 no AIH62 B 265 173 115 1157 1310 103 no AIH63 B 308 265 290 2464 840 104 no AIH64 B 276 179 203 1848 563 105 no AIH65 B 173 119 194 2245 726 106 no AIH66 B 354 156 0 227 109 107 no AIH67 B 73 25 0 267 68 108 no AIH68 B 111 80 42 384 180 109 no AIH69 B 148 90 54 479 235 110 no AIH70 B 229 367 12 3 595 111 no AIH71 B 388 316 0 0 0 112 no AIH72 B 0 5 0 300 323 113 no AIH73 B 0 66 22 92 0 114 no AIH74 B 0 47 0 337 0 115 no AIH75 B 0 256 42 760 0 116 no AIH76 B 107 61 26 391 0 117 no AIH77 B 174 109 57 428 223 118 no AIH78 B 42 46 13 235 319 119 no AIH79 B 180 146 34 362 249 120 no AIH80 B 79 66 57 378 307 121 no AIH81 B 419 86 51 376 533 122 no AIH82 B 448 133 95 631 122 123 no AIH83 B 0 119 49 399 154 124 no AIH84 B 148 90 67 285 167 125 no AIH85 B 11 155 19 231 0 126 no AIH86 B 165 162 167 912 405 127 no AIH87 B 320 150 88 107 4114 128 no AIH88 B 146 87 111 395 238 129 no AIH89 B 90 102 62 112 267 130 no AIH90 B 257 188 171 644 347 131 no AIH91 B 106 60 63 336 0 132 no AIH92 B 1223 584 640 256 0 133 no AIH93 B 519 287 283 0 0 134 no AIH94 B 327 240 101 102 0 135 no AIH95 B 559 2142 59 279 413 136 no AIH96 B 202 201 29 248 0 137 no AIH97 B 212 88 45 472 0 138 no AIH98 B 426 125 68 99 566 139 no AIH99 B 260 135 105 285 34 140 no AIH100 B 371 257 96 528 75 141 no AIH101 B 254 99 105 332 13 142 no AIH102 B 107 86 121 786 168 143 no AIH103 B 265 209 40 328 10 144 no AIH104 B 201 189 31 559 0 145 no AIH105 B 79 63 38 159 2 146 no AIH106 B 111 34 32 343 13 147 no AIH107 B 130 185 0 577 923 148 no AIH108 B 58 29 11 545 0 149 no AIH109 B 49 56 34 390 0 150 no AIH110 B 158 165 68 227 0 151 no AIH111 B 159 205 25 151 32 152 no AIH112 B 144 155 25 600 0 153 no AIH113 B 111 155 83 179 65 154 no AIH114 B 224 115 27 276 67 155 no AIH115 B 85 85 13 123 48 156 no AIH116 B 362 296 11 176 72 157 no AIH117 B 273 264 122 1418 476 158 no AIH118 B 425 402 86 1702 581 159 no AIH119 B 315 418 0 595 305 160 no AIH120 B 463 379 71 626 313 161 no AIH121 B 94 413 46 400 229 162 no AIH122 B 163 115 285 590 213 163 no AIH123 B 0 0 0 1053 362 164 no AIH124 B 0 0 0 430 26 165 no AIH125 B 83 61 299 476 219 166 no AIH126 B 381 303 4 266 376 167 no AIH127 B 253 106 134 626 189 168 no AIH128 B 571 96 31 487 423 169 no AIH129 B 288 298 0 347 411 170 no AIH130 B 135 149 229 864 600 > > demo_data_long <- combiroc_long(data = demo_data) # long format data > > > > > # To visualize the distribution of the expression of each marker. > > distributions <- markers_distribution(data_long = demo_data_long, + boxplot_lim = 1500, y_lim = 0.001, + x_lim = 3000 , signalthr_prediction = FALSE, + case_class = 'A', min_SE = 40, min_SP = 80) > > distributions$Density_plot # density plot > distributions$Density_summary # summary statistics of density plot # A tibble: 2 × 9 Class `# observations` Min Max Median Mean `1st Q` `3rd Q` SD 1 A 200 0 13178 461 814. 233. 825 1427. 2 B 650 0 4114 106 206. 38 266 318. > distributions$ROC # ROC showing signal threshold range ensuring min SE and/or SP Error in `ggplot2::geom_line()`: ! Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error in `.data[["1-specificity"]]`: ! Column `1-specificity` not found in `.data`. Backtrace: ▆ 1. ├─base (local) ``(x) 2. ├─ggplot2:::print.ggplot(x) 3. │ ├─ggplot2::ggplot_build(x) 4. │ └─ggplot2:::ggplot_build.ggplot(x) 5. │ └─ggplot2:::by_layer(...) 6. │ ├─rlang::try_fetch(...) 7. │ │ ├─base::tryCatch(...) 8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 13. │ └─l$compute_aesthetics(d, plot) 14. │ └─ggplot2 (local) compute_aesthetics(..., self = self) 15. │ └─base::lapply(aesthetics, eval_tidy, data = data, env = env) 16. │ └─rlang (local) FUN(X[[i]], ...) 17. ├─1-specificity 18. ├─rlang:::`[[.rlang_data_pronoun`(.data, "1-specificity") 19. │ └─rlang:::data_pronoun_get(...) 20. └─rlang:::abort_data_pronoun(x, call = y) 21. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'combiroc_vignette_1.Rmd' using knitr Quitting from lines 150-151 [ROC] (combiroc_vignette_1.Rmd) Error: processing vignette 'combiroc_vignette_1.Rmd' failed with diagnostics: Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error in `.data[["1-specificity"]]`: ! Column `1-specificity` not found in `.data`. --- failed re-building 'combiroc_vignette_1.Rmd' --- re-building 'combiroc_vignette_2.Rmd' using knitr --- finished re-building 'combiroc_vignette_2.Rmd' SUMMARY: processing the following file failed: 'combiroc_vignette_1.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE