Error(s) in re-building vignettes:
  ...
--- re-building 'Comparing_methods_for_logistic_models.Rmd' using rmarkdown
This is mgcv 1.8-31. 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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'Comparing_methods_for_logistic_models.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building 'Comparing_methods_for_logistic_models.Rmd'

--- re-building 'Diagnostics.Rmd' using rmarkdown
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-36-1.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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-41-1.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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-49-2.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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynamichazard.Rcheck/vign_test/dynamichazard/vignettes/Diagnostics_files/figure-latex/unnamed-chunk-51-1.png" but not available.
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'Diagnostics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- 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
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
a_0 not supplied. IWLS estimates of static glm model is used for random walk models. Otherwise the values are zero
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
--- 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 files failed:
  'Comparing_methods_for_logistic_models.Rmd' 'Diagnostics.Rmd'

Error: Vignette re-building failed.
Execution halted