* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/rmcorr.Rcheck’
* 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 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/rmcorr-00install.html' 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