Error(s) in re-building vignettes:
--- re-building ‘Comparing_methods_for_logistic_models.Rmd’ using rmarkdown
--- finished re-building ‘Comparing_methods_for_logistic_models.Rmd’

--- re-building ‘Diagnostics.Rmd’ using rmarkdown
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-5-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/rossi_hat_plot-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-16-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-17-1.png" but not available.
The magick package is required to crop "figure/replot-rossi_hat_plot-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-20-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-22-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-23-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-24-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-28-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-31-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-32-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-33-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-36-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-39-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-40-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-41-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-42-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-44-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-46-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-48-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-49-1.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-49-2.png" but not available.
The magick package is required to crop "/data/gannet/ripley/R/packages/tests-clang/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-51-1.png" but not available.
--- finished re-building ‘Diagnostics.Rmd’

--- re-building ‘ddhazard.Rnw’ using knitr
fatal: not a git repository (or any parent up to mount point /data)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

Quitting from lines 418-1212 (ddhazard.Rnw)
Error: processing vignette 'ddhazard.Rnw' failed with diagnostics:
there is no package called 'captioner'
--- failed re-building ‘ddhazard.Rnw’

--- re-building ‘Bootstrap_illustration.pdf.asis’ using asis
--- finished re-building ‘Bootstrap_illustration.pdf.asis’

--- re-building ‘Particle_filtering.pdf.asis’ using asis
--- finished re-building ‘Particle_filtering.pdf.asis’

SUMMARY: processing the following file failed:
  ‘ddhazard.Rnw’

Error: Vignette re-building failed.
Execution halted