Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: Removed 319 rows containing missing values (geom_point). 
4: Removed 319 rows containing missing values (geom_tile). 
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: Removed 319 rows containing missing values (geom_point). 
4: Removed 319 rows containing missing values (geom_tile). 
Scale for 'y' is already present. Adding another scale for 'y', which
will replace the existing scale.
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Scale for 'y' is already present. Adding another scale for 'y', which
will replace the existing scale.
In addition: There were 11 warnings (use warnings() to see them)
Scale for 'y' is already present. Adding another scale for 'y', which
will replace the existing scale.
In addition: Warning messages:
1: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
4: Removed 319 rows containing missing values (geom_point). 
5: Removed 319 rows containing missing values (geom_tile). 
6: Removed 319 rows containing missing values (geom_point). 
7: Removed 319 rows containing missing values (geom_tile). 
8: Removed 319 rows containing missing values (geom_point). 
9: Removed 319 rows containing missing values (geom_tile). 
In addition: Warning messages:
1: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
2: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
3: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
4: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
5: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
6: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
7: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
8: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
9: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
--- finished re-building ‘basic-usage.Rmd’

Warning messages:
1: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
2: Removed 957 rows containing missing values (geom_point). 
--- re-building ‘bootstrapping-and-hr-thresholds.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

--- finished re-building ‘bootstrapping-and-hr-thresholds.Rmd’

Warning message:
In kable_markdown(x = c("NA", "NA", "NA", "NA", "NA", "NA", "NA",  :
  The table should have a header (column names)
--- re-building ‘rationale.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: prodlim
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'cowplot'

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

    theme_map

The following object is masked from 'package:ggplot2':

    ggsave

Quitting from lines 59-62 (rationale.Rmd) 
Error: processing vignette 'rationale.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘rationale.Rmd’

SUMMARY: processing the following file failed:
  ‘rationale.Rmd’

Error: Vignette re-building failed.
Execution halted