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.
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Comparing_methods_for_logistic_models.Rmd' failed with diagnostics:
Failed to compile Comparing_methods_for_logistic_models.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Comparing_methods_for_logistic_models.log for more info.
--- failed re-building ‘Comparing_methods_for_logistic_models.Rmd’

--- re-building ‘Diagnostics.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 12 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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.
OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
! LaTeX Error: Environment cslreferences undefined.

Error: processing vignette 'Diagnostics.Rmd' failed with diagnostics:
Failed to compile Diagnostics.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Diagnostics.log for more info.
--- failed 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).
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