• using R Under development (unstable) (2024-10-11 r87227)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-6) 14.2.0     GNU Fortran (Debian 14.2.0-6) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘smdi/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘smdi’ version ‘0.3.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘usethis’
• 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 serialization versions ... OK
• checking whether package ‘smdi’ can be installed ... OK See the install log for details.
• 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 ... [4s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/5s] 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 ... [18s/25s] OK
• checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 ... [17s/24s] OK Examples with CPU (user + system) or elapsed time > 5s                user system elapsed smdi_diagnose 4.273 0.091 6.666 smdi_rf 3.839 0.083 5.643
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [13s/17s] OK   Running ‘testthat.R’ [13s/16s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [204s/273s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘a_data_generation.Rmd’ using rmarkdown Quitting from lines 23-38 [setup] (a_data_generation.Rmd) Error: processing vignette 'a_data_generation.Rmd' failed with diagnostics: there is no package called 'usethis' --- failed re-building ‘a_data_generation.Rmd’ --- re-building ‘b_routine_diagnostics.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-5-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22104 bytes Input file size = 22206 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20281   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 = 19651   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 = 19651 Output IDAT size = 19651 bytes (2453 bytes decrease) Output file size = 19729 bytes (2477 bytes = 11.15% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-6-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 39424 bytes Input file size = 39550 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34520   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 = 34520 Output IDAT size = 34520 bytes (4904 bytes decrease) Output file size = 34598 bytes (4952 bytes = 12.52% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-7-1.png 900x675 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10795 bytes Input file size = 11665 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8693   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 = 8693 Output IDAT size = 8693 bytes (2102 bytes decrease) Output file size = 8771 bytes (2894 bytes = 24.81% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-11-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 54591 bytes Input file size = 54741 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44682   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 = 44682 Output IDAT size = 44682 bytes (9909 bytes decrease) Output file size = 44760 bytes (9981 bytes = 18.23% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/b_routine_diagnostics_files/figure-html/unnamed-chunk-17-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51345 bytes Input file size = 51495 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41754   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 = 41754 Output IDAT size = 41754 bytes (9591 bytes decrease) Output file size = 41832 bytes (9663 bytes = 18.76% decrease) --- finished re-building ‘b_routine_diagnostics.Rmd’ --- re-building ‘c_multivariate_missingness.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/c_multivariate_missingness_files/figure-html/unnamed-chunk-4-1.png 900x675 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8063 bytes Input file size = 8918 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6444   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 = 6444 Output IDAT size = 6444 bytes (1619 bytes decrease) Output file size = 6522 bytes (2396 bytes = 26.87% decrease) --- finished re-building ‘c_multivariate_missingness.Rmd’ --- re-building ‘d_narfcs_sensitivity_analysis.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/d_narfcs_sensitivity_analysis_files/figure-html/unnamed-chunk-3-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49906 bytes Input file size = 50056 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39816   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 = 39816 Output IDAT size = 39816 bytes (10090 bytes decrease) Output file size = 39894 bytes (10162 bytes = 20.30% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/d_narfcs_sensitivity_analysis_files/figure-html/unnamed-chunk-6-1.png 900x675 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 22563 bytes Input file size = 23445 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20419   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 = 20419 Output IDAT size = 20419 bytes (2144 bytes decrease) Output file size = 20497 bytes (2948 bytes = 12.57% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/d_narfcs_sensitivity_analysis_files/figure-html/unnamed-chunk-8-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53311 bytes Input file size = 53461 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 41158   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 = 41158 Output IDAT size = 41158 bytes (12153 bytes decrease) Output file size = 41236 bytes (12225 bytes = 22.87% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smdi.Rcheck/vign_test/smdi/vignettes/d_narfcs_sensitivity_analysis_files/figure-html/unnamed-chunk-10-1.png 900x675 pixels, 3x8 bits/pixel, RGB Input IDAT size = 52477 bytes Input file size = 52627 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39892   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 = 39892 Output IDAT size = 39892 bytes (12585 bytes decrease) Output file size = 39970 bytes (12657 bytes = 24.05% decrease) --- finished re-building ‘d_narfcs_sensitivity_analysis.Rmd’ --- re-building ‘smdi.Rmd’ using rmarkdown --- finished re-building ‘smdi.Rmd’ SUMMARY: processing the following file failed:   ‘a_data_generation.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR