• using R Under development (unstable) (2025-02-15 r87723)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘rmcorr/DESCRIPTION’ ... OK
• this is package ‘rmcorr’ version ‘0.7.0’
• 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 whether package ‘rmcorr’ can be installed ... OK See the install log for details.
• checking package directory ... 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 ... 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 ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/13s] OK   Running ‘testthat.R’ [10s/13s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [81s/105s] ERROR Error(s) in re-building vignettes: --- re-building ‘CI_fix.Rmd’ using rmarkdown --- finished re-building ‘CI_fix.Rmd’ --- re-building ‘FAQ_and_limitations.Rmd’ using rmarkdown --- finished re-building ‘FAQ_and_limitations.Rmd’ --- re-building ‘New_rmcorr_paper_analyses_figures.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-3-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40261 bytes Input file size = 40387 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31777   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 = 31777 Output IDAT size = 31777 bytes (8484 bytes decrease) Output file size = 31855 bytes (8532 bytes = 21.13% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-4-1.png 768x768 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43872 bytes Input file size = 44010 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32123   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 = 32123 Output IDAT size = 32123 bytes (11749 bytes decrease) Output file size = 32201 bytes (11809 bytes = 26.83% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-5-1.png 1152x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24262 bytes Input file size = 24364 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21811   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 = 21515   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 = 21515 Output IDAT size = 21515 bytes (2747 bytes decrease) Output file size = 21593 bytes (2771 bytes = 11.37% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-6-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 50894 bytes Input file size = 51044 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 = 47267   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 = 47267 Output IDAT size = 47267 bytes (3627 bytes decrease) Output file size = 47345 bytes (3699 bytes = 7.25% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-7-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 72200 bytes Input file size = 72374 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56271   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 = 56271 Output IDAT size = 56271 bytes (15929 bytes decrease) Output file size = 56349 bytes (16025 bytes = 22.14% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-8-1.png 864x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32545 bytes Input file size = 32659 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24935   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 = 24935 Output IDAT size = 24935 bytes (7610 bytes decrease) Output file size = 25013 bytes (7646 bytes = 23.41% decrease) Quitting from lines 647-701 [unnamed-chunk-9] (New_rmcorr_paper_analyses_figures.Rmd) Error: processing vignette 'New_rmcorr_paper_analyses_figures.Rmd' failed with diagnostics: Profiling over both the residual variance and fixed effects is not numerically consistent with profiling over the fixed effects only (relative difference: 1); consider adjusting devmatchtol --- failed re-building ‘New_rmcorr_paper_analyses_figures.Rmd’ --- re-building ‘compcor.Rmd’ using rmarkdown --- finished re-building ‘compcor.Rmd’ --- re-building ‘estimates_w_NaN.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/estimates_w_NaN_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4840 bytes Input file size = 5695 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4266   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 = 4266 Output IDAT size = 4266 bytes (574 bytes decrease) Output file size = 4344 bytes (1351 bytes = 23.72% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/estimates_w_NaN_files/figure-html/unnamed-chunk-3-2.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 6479 bytes Input file size = 6557 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4863   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 = 4863 Output IDAT size = 4863 bytes (1616 bytes decrease) Output file size = 4941 bytes (1616 bytes = 24.65% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/estimates_w_NaN_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13408 bytes Input file size = 13498 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10162   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 = 10162 Output IDAT size = 10162 bytes (3246 bytes decrease) Output file size = 10240 bytes (3258 bytes = 24.14% decrease) --- finished re-building ‘estimates_w_NaN.Rmd’ --- re-building ‘model_diag.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/model_diag_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49346 bytes Input file size = 49496 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31391   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 = 31391 Output IDAT size = 31391 bytes (17955 bytes decrease) Output file size = 31469 bytes (18027 bytes = 36.42% decrease) --- finished re-building ‘model_diag.Rmd’ --- re-building ‘overfitting.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/overfitting_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29440 bytes Input file size = 29554 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20809   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 = 20809 Output IDAT size = 20809 bytes (8631 bytes decrease) Output file size = 20887 bytes (8667 bytes = 29.33% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/overfitting_files/figure-html/unnamed-chunk-5-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35625 bytes Input file size = 35751 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26855   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 = 26855 Output IDAT size = 26855 bytes (8770 bytes decrease) Output file size = 26933 bytes (8818 bytes = 24.67% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/overfitting_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15905 bytes Input file size = 15995 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11135   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 = 11135 Output IDAT size = 11135 bytes (4770 bytes decrease) Output file size = 11213 bytes (4782 bytes = 29.90% decrease) --- finished re-building ‘overfitting.Rmd’ --- re-building ‘repro_bootstrapping.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/repro_bootstrapping_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13369 bytes Input file size = 13459 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9945   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 = 9945 Output IDAT size = 9945 bytes (3424 bytes decrease) Output file size = 10023 bytes (3436 bytes = 25.53% decrease) --- finished re-building ‘repro_bootstrapping.Rmd’ --- re-building ‘rmcorr_mat.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/rmcorr_mat_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30648 bytes Input file size = 30762 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24895   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 = 24895 Output IDAT size = 24895 bytes (5753 bytes decrease) Output file size = 24973 bytes (5789 bytes = 18.82% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck/vign_test/rmcorr/vignettes/rmcorr_mat_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20913 bytes Input file size = 21015 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17457   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 = 17457 Output IDAT size = 17457 bytes (3456 bytes decrease) Output file size = 17535 bytes (3480 bytes = 16.56% decrease) --- finished re-building ‘rmcorr_mat.Rmd’ SUMMARY: processing the following file failed:   ‘New_rmcorr_paper_analyses_figures.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR