* using log directory ‘/Users/ripley/R/packages/tests-devel/dynamichazard.Rcheck’
* using R Under development (unstable) (2023-08-26 r85014)
* using platform: aarch64-apple-darwin22.6.0
* R was compiled by
    Apple clang version 15.0.0 (clang-1500.0.40.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.5.1
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘dynamichazard/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dynamichazard’ version ‘1.0.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘captioner’
* 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 ‘dynamichazard’ can be installed ... [106s/100s] OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX14.0.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.7Mb
    libs   1.8Mb
* 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 R 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 whether startup messages can be suppressed ... 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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 ...
  Running ‘testthat.R’ [12s/12s]
 [12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [18s/19s] ERROR
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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 "/Users/ripley/R/packages/tests-devel/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 of the parent directories): .git

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

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/ripley/R/packages/tests-devel/dynamichazard.Rcheck/00check.log’
for details.

      162.67 real       153.78 user        11.60 sys