##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data nucleR
###
##############################################################################
##############################################################################


* checking for file ‘nucleR/DESCRIPTION’ ... OK
* preparing ‘nucleR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘nucleR.Rmd’ using rmarkdown
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: GenomeInfoDb
reading file /private/tmp/Rtmp4FQArf/Rinst14b57314a58ba/nucleR/extdata/cellCycleM_chrII_5000-25000.bam
processing flags
processing strand +
processing strand -
Warning in exp - (ctr - mean(ctr[ctr != 0])) :
  longer object length is not a multiple of shorter object length
Warning: Removed 87 row(s) containing missing values (geom_path).
Warning: Removed 1001 rows containing missing values (position_stack).
[WARNING] Could not parse YAML metadata at line 21 column 1: :2:77: Unexpected '
  '
pandoc-citeproc: reference Flores2011 not found
pandoc-citeproc: reference Lee2007 not found
pandoc-citeproc: reference Mavrich2008 not found
pandoc-citeproc: reference Yuan2005 not found
pandoc-citeproc: reference Liu2007 not found
pandoc-citeproc: reference Lee2007 not found
pandoc-citeproc: reference Yuan2005 not found
pandoc-citeproc: reference Kuan2009 not found
pandoc-citeproc: reference Schones2008 not found
pandoc-citeproc: reference Xi2010 not found
pandoc-citeproc: reference Kaplan2009 not found
pandoc-citeproc: reference Lee2007 not found
pandoc-citeproc: reference Deniz2011 not found
pandoc-citeproc: reference Deniz2011 not found
pandoc-citeproc: reference Lee2007 not found
pandoc-citeproc: reference Kuan2009 not found
pandoc-citeproc: reference Chen2010 not found
pandoc-citeproc: reference Xi2010 not found
pandoc-citeproc: reference Yuan2005 not found
pandoc-citeproc: reference Jiang2009 not found
pandoc-citeproc: reference Smith1999 not found
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TeX Live.
I was unable to find any missing LaTeX packages from the error log nucleR.log.
! Undefined control sequence.
l.76 \definecolor
                 {fgcolor}{rgb}{0.251, 0.251, 0.251} 

Error: processing vignette 'nucleR.Rmd' failed with diagnostics:
LaTeX failed to compile /private/tmp/Rtmp4FQArf/Rbuild14b5776911e06/nucleR/vignettes/nucleR.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See nucleR.log for more info.
--- failed re-building ‘nucleR.Rmd’

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

Error: Vignette re-building failed.
Execution halted