Error(s) in re-building vignettes:
--- re-building ‘BeeBDC_main.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpjZ9R4x/Data_acquisition_workflow (probably via setwd()). It will be restored to /Volumes/Builds/packages/big-sur-arm64/results/4.2/BeeBDC.Rcheck/vign_test/BeeBDC/vignettes. See the Note section in ?knitr::knit
Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.0'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:5:1: unexpected symbol
4: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Only keep a subset of columns from bees3sp.HaHaHa_EnD_TiDy_IdEnTiFiEr")
5: bees3sp
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.4'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:6:1: unexpected string constant
5: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Keep all plus some at the bottom..HaHaHa_EnD_TiDy_IdEnTiFiEr")
6: "Event"
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.5a'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Create a Tibble of common issues in country names and their replacements.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: commonProblems
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.5b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:7:1: unexpected symbol
6: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# How many rows to process at a time.HaHaHa_EnD_TiDy_IdEnTiFiEr")
7: stepSize
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.6'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:6:1: unexpected symbol
5: 
6: data
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.7'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# bdc_coordinates_transposed inputs.HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: data
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.11'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# DON'T flag if in the following dataSource(s).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: excludeDataSource
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.13a'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:6:1: unexpected symbol
5: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# These are the columns that will be kept along with the flags.HaHaHa_EnD_TiDy_IdEnTiFiEr")
6: idColumns
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '3.13b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Don't filter these columns (or NULL).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: dontFilterThese
   ^

trying URL 'https://figshare.com/ndownloader/files/42320595?private_link=bce1f92848c2ced313ee'
Content type 'application/octet-stream' length 1104632 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Warning in eng_r(options) :
  Failed to tidy R code in chunk '4.2ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:1:54: unexpected SPECIAL
1: database <- BeeBDC :: harmoniseR ( path = DataPath , %%
                                                         ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.2ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:7:20: unexpected SPECIAL
6: species = "scientificName" ,
7: countries = NULL , %%
                      ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.3'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The minimum number of repeats needed to find a sequence in for flagging.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: minRepeats
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.3iv'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:5:1: unexpected symbol
4: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Select the columns of interest.HaHaHa_EnD_TiDy_IdEnTiFiEr")
5: dplyr
   ^

trying URL 'https://figshare.com/ndownloader/files/42320598?private_link=bce1f92848c2ced313ee'
Content type 'application/octet-stream' length 764612 bytes (746 KB)
==================================================
downloaded 746 KB

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.5ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:8:1: unexpected symbol
7: 
8: scale
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.6ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:2:124: unexpected SPECIAL
1: check_space %>                                                                                %
2: dplyr :: filter ( .summary == FALSE ) %>                                                                                % %%
                                                                                                                              ^

Warning in doTryCatch(return(expr), name, parentenv, handler) :
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Warning in eng_r(options) :
  Failed to tidy R code in chunk '6.1'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Years above this are removed (from the recovered dates only).HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: maxYear
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '6.4'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Don't filter these columns (or NULL).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: dontFilterThese
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '7.1'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:5:1: unexpected symbol
4: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# options are 'ID','collectionInfo', or 'both'.HaHaHa_EnD_TiDy_IdEnTiFiEr")
5: duplicatedBy
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '8.3'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:6:1: unexpected symbol
5: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Remove the filtering columns?.HaHaHa_EnD_TiDy_IdEnTiFiEr")
6: removeFilterColumns
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '9.1iv'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The duplicate data from the dupeSummary function output  .HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: dupeData
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '9.2ii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The outPath to save the plot as.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: outPath
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '9.3'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Colours in order of pass (TRUE), fail (FALSE), and NA.HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: flagColours
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '9.4b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:3:1: unexpected symbol
2: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# occurrence data.HaHaHa_EnD_TiDy_IdEnTiFiEr")
3: data
   ^

Could not fetch https://photos.smugmug.com/photos/i-Xt3tN8L/0/X5/i-Xt3tN8L-X5.jpg
HttpExceptionRequest Request {
  host                 = "photos.smugmug.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/photos/i-Xt3tN8L/0/X5/i-Xt3tN8L-X5.jpg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed (Error_Protocol ("certificate has unknown CA",True,UnknownCa))))
Error: processing vignette 'BeeBDC_main.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘BeeBDC_main.Rmd’

--- re-building ‘basic_workflow.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpjZ9R4x/Data_acquisition_workflow (probably via setwd()). It will be restored to /Volumes/Builds/packages/big-sur-arm64/results/4.2/BeeBDC.Rcheck/vign_test/BeeBDC/vignettes. See the Note section in ?knitr::knit
trying URL 'https://figshare.com/ndownloader/files/42320595?private_link=bce1f92848c2ced313ee'
Content type 'application/octet-stream' length 1104632 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Warning in eng_r(options) :
  Failed to tidy R code in chunk '4.1'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:4:1: unexpected symbol
3: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Choose the columns to NOT filter (or NULL to filter all columns).HaHaHa_EnD_TiDy_IdEnTiFiEr")
4: dontFilterThese
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '4.2'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:8:1: unexpected symbol
7: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# 10 km here.HaHaHa_EnD_TiDy_IdEnTiFiEr")
8: threshold
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '4.2b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:9:1: unexpected symbol
8: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# Select the input dataset to filter.HaHaHa_EnD_TiDy_IdEnTiFiEr")
9: data
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.1iii'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:9:1: unexpected symbol
8: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The duplicate data from the dupeSummary function output  .HaHaHa_EnD_TiDy_IdEnTiFiEr")
9: dupeData
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.2'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:9:1: unexpected symbol
8: invisible(".BeGiN_TiDy_IdEnTiFiEr_HaHaHa# The outPath to save the plot as.HaHaHa_EnD_TiDy_IdEnTiFiEr")
9: outPath
   ^

Warning in eng_r(options) :
  Failed to tidy R code in chunk '5.3b'. Reason:
Error in base::parse(text = code, keep.source = keep.source) : 
  <text>:6:1: unexpected symbol
5: 
6: data
   ^

--- finished re-building ‘basic_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted