Error(s) in re-building vignettes:
--- re-building ‘all_tables_examples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(obstruct.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in chisq.test(extent.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, extent.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(obstruct.factor, extent.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, mort_5yr) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(obstruct.factor, mort_5yr) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Waiting for profiling to be done...
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
P-value for lmer is estimate assuming t-distribution is normal. Bootstrap for final publication.
Note: dependent includes missing data. These are dropped.
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00357214 (tol = 0.002, component 1)
P-value for lmer is estimate assuming t-distribution is normal. Bootstrap for final publication.
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Dependent variable is a survival object
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'all_tables_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘all_tables_examples.Rmd’

--- re-building ‘bootstrap.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'bootstrap.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘bootstrap.Rmd’

--- re-building ‘data_prep.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'data_prep.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘data_prep.Rmd’

--- re-building ‘export.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Note: dependent includes missing data. These are dropped.
Warning in chisq.test(extent.factor, differ.factor) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
Warning in chisq.test(extent.factor, differ.factor) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
Warning: Factor `differ.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'export.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘export.Rmd’

--- re-building ‘finalfit.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'finalfit.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘finalfit.Rmd’

--- re-building ‘missing.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'mice'

The following objects are masked from 'package:base':

    cbind, rbind

Note: Using an external vector in selections is ambiguous.
ℹ Use `all_of(dependent)` instead of `dependent` to silence this message.
ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.
Note: Using an external vector in selections is ambiguous.
ℹ Use `all_of(explanatory)` instead of `explanatory` to silence this message.
ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This message is displayed once per session.
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning: Factor `smoking_mar` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning: Removed 8 rows containing missing values (geom_errorbarh).
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning: Factor `smoking_mar` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Note: dependent includes missing data. These are dropped.
Warning: Factor `obstruct.factor` contains implicit NA, consider using `forcats::fct_explicit_na`
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
Waiting for profiling to be done...
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'missing.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘missing.Rmd’

--- re-building ‘survival.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'survival.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘survival.Rmd’

SUMMARY: processing the following files failed:
  ‘all_tables_examples.Rmd’ ‘bootstrap.Rmd’ ‘data_prep.Rmd’
  ‘export.Rmd’ ‘finalfit.Rmd’ ‘missing.Rmd’ ‘survival.Rmd’

Error: Vignette re-building failed.
Execution halted