Error(s) in re-building vignettes:
--- re-building 'Comparing_methods_for_logistic_models.Rmd' using rmarkdown
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
--- finished re-building 'Comparing_methods_for_logistic_models.Rmd'

--- re-building 'Diagnostics.Rmd' using rmarkdown
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-5-1.png" but not available.
Loading required package: survival
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/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 "d:/RCompile/CRANpkg/local/4.1/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 "d:/RCompile/CRANpkg/local/4.1/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 "d:/RCompile/CRANpkg/local/4.1/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 "d:/RCompile/CRANpkg/local/4.1/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-16-1.png" but not available.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/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.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-20-1.png" but not available.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
Warning in ddhazard_fit_cpp(a_0 = a_0, Q_0 = Q_0, F_ = F., verbose = verbose,  :
  EM algorithm did not converge within the n_max number of iterations
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-22-1.png" but not available.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
Warning in ddhazard_fit_cpp(a_0 = a_0, Q_0 = Q_0, F_ = F., verbose = verbose,  :
  EM algorithm did not converge within the n_max number of iterations
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-23-1.png" but not available.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
The magick package is required to crop "d:/RCompile/CRANpkg/local/4.1/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 "d:/RCompile/CRANpkg/local/4.1/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-28-1.png" but not available.
Quitting from lines 564-565 (Diagnostics.Rmd) 
Error: processing vignette 'Diagnostics.Rmd' failed with diagnostics:
all(abs(stat_res$residuals) < 1.96) is not TRUE
--- failed re-building 'Diagnostics.Rmd'

--- re-building 'ddhazard.Rnw' using knitr
fatal: Not a git repository (or any of the parent directories): .git
Warning in system("git rev-parse --short HEAD", intern = TRUE) :
  running command 'git rev-parse --short HEAD' had status 128
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
--- finished 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:
  'Diagnostics.Rmd'

Error: Vignette re-building failed.
Execution halted