Error in re-building vignettes:
  ...
Loading required package: lattice
Loading required package: grid
Loading required package: ggplot2
Package hyperSpec, version 0.99-20180627

To get started, try
   vignette ("hyperspec")
   package?hyperSpec 
   vignette (package = "hyperSpec")

If you use this package please cite it appropriately.
   citation("hyperSpec")
will give you the correct reference.

The project homepage is http://hyperspec.r-forge.r-project.org


start: 300 support points
Iteration 1: 146 support points
Iteration 2: 85 support points
Iteration 3: 44 support points
Iteration 4: 26 support points
Iteration 5: 12 support points
Iteration 6: 7 support points
Iteration 7: 2 support points
Warning in max(x@wavelength) :
  no non-missing arguments to max; returning -Inf
Warning in min(x@wavelength) :
  no non-missing arguments to min; returning Inf
Warning in max(x@wavelength) :
  no non-missing arguments to max; returning -Inf
Warning in min(x@wavelength) :
  no non-missing arguments to min; returning Inf
Iteration 8: 0 support points
spectrum      1:     2 support points, noise = 0.0,   8 iterations
Fitting with npts.min = 15

start: 300 support points
spectrum      1:    20 support points, noise = 0.0,   5 iterations
Fitting with npts.min = 15

start: 300 support points
spectrum      1:    26 support points, noise = 0.0,   5 iterations
Fitting with npts.min = 15

start: 300 support points
spectrum      1:    25 support points, noise = 0.0,   5 iterations
Fitting with npts.min = 5

start: 100 support points
spectrum      1:    97 support points, noise = 4.0,   2 iterations
Fitting with npts.min = 15

start: 300 support points
Iteration 1: 153 support points
Iteration 2: 93 support points
Iteration 3: 54 support points
Iteration 4: 38 support points
Iteration 5: 32 support points
Iteration 6: 29 support points
Iteration 7: 29 support points
spectrum      1:    29 support points, noise = 15.0,   7 iterations
Read 362 items
Read 362 items
Read 362 items
Read 362 items
Read 362 items
Read 362 items
Warning in min(abs(diff(x@wavelength))) :
  no non-missing arguments to min; returning Inf
Warning in min(abs(diff(x@wavelength))) :
  no non-missing arguments to min; returning Inf
Loading required namespace: mvtnorm
Loading required package: MASS
Warning in predict.lda(lda, chondro) :
  variable names in 'newdata' do not match those in 'object'
Warning in rm(chondro) : object 'chondro' not found
Loading required package: baseline

Attaching package: 'baseline'

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

    getCall

Warning in scores[, , 1:10] %*% loadings[1:10] :
  Dropping column(s) of y: filename, measurement
Loading required package: rgl
plot chunk
Warning in (function (object, model = spc ~ c, groups = NULL, func = NULL,  :
  Intensity at first wavelengh only is used.
Warning in hyperSpec:::.levelplot(x, data, ...) :
  Only first wavelength is used for plotting
Loading required namespace: deldir

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


Warning in plotc(x, ...) : Intensity at first wavelengh only is used.
Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col,  :
  'x' values are not equispaced; output may be wrong
Warning in hyperSpec:::.levelplot(x, data, ...) :
  Only first wavelength is used for plotting
Loading required package: latticeExtra
Loading required package: RColorBrewer

Attaching package: 'latticeExtra'

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

    layer

Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col,  :
  'x' values are not equispaced; output may be wrong
Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col,  :
  'y' values are not equispaced; output may be wrong
Loading required package: rgl
Warning: Ignoring unknown aesthetics: y

Error: processing vignette 'plotting.Rnw' failed with diagnostics:
 chunk 81 (label = ggplot2-do) 
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_reg
Execution halted