• using R Under development (unstable) (2024-10-04 r87206)
• 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 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 ... [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/1s] 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 ... [33s/41s] OK
• checking Rd files ... [1s/1s] 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:   ed_laplace_ofv.Rd: fdHess Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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 ... [19s/24s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [12s/15s] OK   Running ‘testthat.R’ [12s/14s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [111s/146s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘examples.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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 ... [8s/11s] OK
• checking HTML version of manual ... [4s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE