* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck’ * using R Under development (unstable) (2025-06-12 r88305) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘MAPCtools/DESCRIPTION’ ... OK * this is package ‘MAPCtools’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Lars Vatten ’ New submission Possibly misspelled words in DESCRIPTION: MAPC (2:50, 7:103) Suggests or Enhances not in mainstream repositories: INLA * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘INLA’ * 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 ‘MAPCtools’ can be installed ... [4s/4s] 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 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 ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/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 use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING print: function(x, ...) print.mapc: function(object, ...) summary: function(object, ...) summary.mapc: function(x, ...) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [6s/6s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plot_missing_data.Rd: ggplot Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Unknown package ‘INLA’ in Rd xrefs * 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 ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/6s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [10s/10s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘quickstart.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-3-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35113 bytes Input file size = 35239 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26639 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26639 Output IDAT size = 26639 bytes (8474 bytes decrease) Output file size = 26717 bytes (8522 bytes = 24.18% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-4-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38284 bytes Input file size = 38410 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30216 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30216 Output IDAT size = 30216 bytes (8068 bytes decrease) Output file size = 30294 bytes (8116 bytes = 21.13% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-4-2.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38181 bytes Input file size = 38307 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30275 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30275 Output IDAT size = 30275 bytes (7906 bytes decrease) Output file size = 30353 bytes (7954 bytes = 20.76% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-5-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 75730 bytes Input file size = 75916 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70218 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 70218 Output IDAT size = 70218 bytes (5512 bytes decrease) Output file size = 70296 bytes (5620 bytes = 7.40% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-5-2.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 67295 bytes Input file size = 67469 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59061 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59061 Output IDAT size = 59061 bytes (8234 bytes decrease) Output file size = 59139 bytes (8330 bytes = 12.35% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-6-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29652 bytes Input file size = 29766 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22836 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22836 Output IDAT size = 22836 bytes (6816 bytes decrease) Output file size = 22914 bytes (6852 bytes = 23.02% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-6-2.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29342 bytes Input file size = 29456 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22625 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22625 Output IDAT size = 22625 bytes (6717 bytes decrease) Output file size = 22703 bytes (6753 bytes = 22.93% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-7-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 90309 bytes Input file size = 90519 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 87430 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 87430 Output IDAT size = 87430 bytes (2879 bytes decrease) Output file size = 87508 bytes (3011 bytes = 3.33% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-7-2.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 85838 bytes Input file size = 86036 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 82899 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 82899 Output IDAT size = 82899 bytes (2939 bytes decrease) Output file size = 82977 bytes (3059 bytes = 3.56% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-8-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 36873 bytes Input file size = 36999 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28171 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28171 Output IDAT size = 28171 bytes (8702 bytes decrease) Output file size = 28249 bytes (8750 bytes = 23.65% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-8-2.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38590 bytes Input file size = 38716 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29215 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29215 Output IDAT size = 29215 bytes (9375 bytes decrease) Output file size = 29293 bytes (9423 bytes = 24.34% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35094 bytes Input file size = 35220 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26111 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26111 Output IDAT size = 26111 bytes (8983 bytes decrease) Output file size = 26189 bytes (9031 bytes = 25.64% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-10-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 34230 bytes Input file size = 34356 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28154 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28154 Output IDAT size = 28154 bytes (6076 bytes decrease) Output file size = 28232 bytes (6124 bytes = 17.83% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-10-2.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30299 bytes Input file size = 30413 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26075 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26075 Output IDAT size = 26075 bytes (4224 bytes decrease) Output file size = 26153 bytes (4260 bytes = 14.01% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/MAPCtools.Rcheck/vign_test/MAPCtools/vignettes/quickstart_files/figure-html/unnamed-chunk-10-3.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38085 bytes Input file size = 38211 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30927 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30927 Output IDAT size = 30927 bytes (7158 bytes decrease) Output file size = 31005 bytes (7206 bytes = 18.86% decrease) Quitting from quickstart.Rmd:219-230 [unnamed-chunk-12] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `fit_MAPC()`: ! This function requires the INLA package. Please install it using: install.packages("INLA", repos = c(INLA = "https://inla.r-inla-download.org/R/stable")) --- Backtrace: ▆ 1. └─MAPCtools::fit_MAPC(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'quickstart.Rmd' failed with diagnostics: This function requires the INLA package. Please install it using: install.packages("INLA", repos = c(INLA = "https://inla.r-inla-download.org/R/stable")) --- failed re-building ‘quickstart.Rmd’ SUMMARY: processing the following file failed: ‘quickstart.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs