* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck’ * using R version 4.4.1 Patched (2024-08-05 r86980) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-3) 14.2.0 GNU Fortran (Debian 14.2.0-3) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘PopED/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PopED’ version ‘0.6.0’ * package encoding: UTF-8 * 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 serialization versions ... OK * checking whether package ‘PopED’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/PopED-00install.html' 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 ... [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 whether startup messages can be suppressed ... [1s/2s] 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 ... [50s/61s] OK * checking Rd files ... [1s/2s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [29s/33s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [19s/25s] OK Running ‘testthat.R’ [19s/25s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [177s/220s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘examples.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_multi-response_model-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15867 bytes Input file size = 16737 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14285 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 = 14285 Output IDAT size = 14285 bytes (1582 bytes decrease) Output file size = 14363 bytes (2374 bytes = 14.18% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_ODE_model-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 24719 bytes Input file size = 25613 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22151 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 = 18259 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 18172 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 18172 Output IDAT size = 18172 bytes (6547 bytes decrease) Output file size = 18250 bytes (7363 bytes = 28.75% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_different_dose_regimen-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 66345 bytes Input file size = 66519 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55125 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 = 55125 Output IDAT size = 55125 bytes (11220 bytes decrease) Output file size = 55203 bytes (11316 bytes = 17.01% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/unnamed-chunk-24-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9788 bytes Input file size = 10658 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7999 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 = 7999 Output IDAT size = 7999 bytes (1789 bytes decrease) Output file size = 8077 bytes (2581 bytes = 24.22% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_IOV_with_IIV-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 45470 bytes Input file size = 45608 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 = 41109 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 = 41109 Output IDAT size = 41109 bytes (4361 bytes decrease) Output file size = 41187 bytes (4421 bytes = 9.69% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_with_cov_matrix-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14141 bytes Input file size = 15011 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12196 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 = 12196 Output IDAT size = 12196 bytes (1945 bytes decrease) Output file size = 12274 bytes (2737 bytes = 18.23% decrease) Quitting from lines 971-988 [unnamed-chunk-46] (examples.Rmd) Error: processing vignette 'examples.Rmd' failed with diagnostics: incorrect number of dimensions --- failed re-building ‘examples.Rmd’ --- re-building ‘intro-poped.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_without_BSV-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42539 bytes Input file size = 42677 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36724 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 = 36724 Output IDAT size = 36724 bytes (5815 bytes decrease) Output file size = 36802 bytes (5875 bytes = 13.77% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_with_BSV-1.png 576x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 17208 bytes Input file size = 18090 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15886 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 = 15397 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 15299 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 15299 Output IDAT size = 15299 bytes (1909 bytes decrease) Output file size = 15377 bytes (2713 bytes = 15.00% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_optimal_design-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42239 bytes Input file size = 42377 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36107 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 = 36107 Output IDAT size = 36107 bytes (6132 bytes decrease) Output file size = 36185 bytes (6192 bytes = 14.61% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_efficiency_windows-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 137872 bytes Input file size = 138142 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 121576 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 = 120826 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 = 120826 Output IDAT size = 120826 bytes (17046 bytes decrease) Output file size = 120904 bytes (17238 bytes = 12.48% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_discrete_optimization-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42505 bytes Input file size = 42643 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36713 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 = 36713 Output IDAT size = 36713 bytes (5792 bytes decrease) Output file size = 36791 bytes (5852 bytes = 13.72% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/unnamed-chunk-16-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22122 bytes Input file size = 22224 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17836 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 = 17836 Output IDAT size = 17836 bytes (4286 bytes decrease) Output file size = 17914 bytes (4310 bytes = 19.39% decrease) --- finished re-building ‘intro-poped.Rmd’ SUMMARY: processing the following file failed: ‘examples.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [12s/16s] OK * checking HTML version of manual ... [6s/9s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR