Error(s) in re-building vignettes:
--- re-building 'MeBrPlot.Rmd' using rmarkdown
--- finished re-building 'MeBrPlot.Rmd'

--- re-building 'countDists.Rmd' using rmarkdown
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/plot-gph12-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/cfDBI-BB-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/plot-binAB-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/cfsim-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/cfq2-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/rqmales-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/plot-poisAB-1.png" but not available.
The magick package is required to crop "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/qra/qra.Rcheck/vign_test/qra/vignettes/countDists_files/figure-html/wormpois-1.png" but not available.
--- finished re-building 'countDists.Rmd'

--- re-building 'timeMortality.Rmd' using rmarkdown
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Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in fitTMB(TMBStruc) :
  Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in fitTMB(TMBStruc) :
  Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in (function (start, objective, gradient = NULL, hessian = NULL,  :
  NA/NaN function evaluation
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0),  :
  'giveCsparse' has been deprecated; setting 'repr = "T"' for you
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
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Quitting from lines 1103-1114 (timeMortality.Rmd) 
Error: processing vignette 'timeMortality.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'timeMortality.Rmd'

SUMMARY: processing the following file failed:
  'timeMortality.Rmd'

Error: Vignette re-building failed.
Execution halted