Error(s) in re-building vignettes:
--- re-building ‘detectRUNS.vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
You are using the method: SLIDING WINDOWS
Analysing Runs of Homozygosity (ROHom)
Window size: 15
Threshold for calling SNP in a Run: 0.05
N. of RUNS for individual H114 is: 15
N. of RUNS for individual H115 is: 19
N. of RUNS for individual H116 is: 17
N. of RUNS for individual H26 is: 18
N. of RUNS for individual H32 is: 10
N. of RUNS for individual H38 is: 4
N. of RUNS for individual H44 is: 5
N. of RUNS for individual H56 is: 5
N. of RUNS for individual H50 is: 16
N. of RUNS for individual H27 is: 12
N. of RUNS for individual H33 is: 15
N. of RUNS for individual H39 is: 6
N. of RUNS for individual H45 is: 13
N. of RUNS for individual H51 is: 21
N. of RUNS for individual H57 is: 11
N. of RUNS for individual H28 is: 9
N. of RUNS for individual H34 is: 8
N. of RUNS for individual H40 is: 12
N. of RUNS for individual H46 is: 19
N. of RUNS for individual H52 is: 7
N. of RUNS for individual H58 is: 4
N. of RUNS for individual H29 is: 11
N. of RUNS for individual H35 is: 20
N. of RUNS for individual H41 is: 13
N. of RUNS for individual H47 is: 13
N. of RUNS for individual H53 is: 13
N. of RUNS for individual H59 is: 12
N. of RUNS for individual H30 is: 7
N. of RUNS for individual H42 is: 6
N. of RUNS for individual H48 is: 14
N. of RUNS for individual H54 is: 15
N. of RUNS for individual H60 is: 8
N. of RUNS for individual H31 is: 5
N. of RUNS for individual H37 is: 7
N. of RUNS for individual H43 is: 3
N. of RUNS for individual H49 is: 11
N. of RUNS for individual H55 is: 18
N. of RUNS for individual H1 is: 8
N. of RUNS for individual H9 is: 7
N. of RUNS for individual H17 is: 19
N. of RUNS for individual H2 is: 11
N. of RUNS for individual H10 is: 8
N. of RUNS for individual H19 is: 10
N. of RUNS for individual H3 is: 8
N. of RUNS for individual H11 is: 8
N. of RUNS for individual H20 is: 23
N. of RUNS for individual H4 is: 7
N. of RUNS for individual H12 is: 8
N. of RUNS for individual H21 is: 19
N. of RUNS for individual H13 is: 11
N. of RUNS for individual H22 is: 20
N. of RUNS for individual H6 is: 7
N. of RUNS for individual H14 is: 9
N. of RUNS for individual H7 is: 19
N. of RUNS for individual H15 is: 9
N. of RUNS for individual H24 is: 10
N. of RUNS for individual H8 is: 12
N. of RUNS for individual H16 is: 22
N. of RUNS for individual H25 is: 14
N. of RUNS for individual H64 is: 21
N. of RUNS for individual H62 is: 11
N. of RUNS for individual H63 is: 6
N. of RUNS for individual H118 is: 19
N. of RUNS for individual H119 is: 15
N. of RUNS for individual H120 is: 14
N. of RUNS for individual H121 is: 22
N. of RUNS for individual H122 is: 16
N. of RUNS for individual H123 is: 10
N. of RUNS for individual H124 is: 18
N. of RUNS for individual H125 is: 14
N. of RUNS for individual H126 is: 16
N. of RUNS for individual H127 is: 20
N. of RUNS for individual H128 is: 19
N. of RUNS for individual H129 is: 9
N. of RUNS for individual H130 is: 21
N. of RUNS for individual H131 is: 21
N. of RUNS for individual H132 is: 17
N. of RUNS for individual H133 is: 19
N. of RUNS for individual H134 is: 16
N. of RUNS for individual H135 is: 15
N. of RUNS for individual H136 is: 10
N. of RUNS for individual H137 is: 19
N. of RUNS for individual H138 is: 11
N. of RUNS for individual H139 is: 19
N. of RUNS for individual H140 is: 15
N. of RUNS for individual H141 is: 19
N. of RUNS for individual H142 is: 17
N. of RUNS for individual H143 is: 15
N. of RUNS for individual H144 is: 14
N. of RUNS for individual H145 is: 17
N. of RUNS for individual H146 is: 18
N. of RUNS for individual H147 is: 13
N. of RUNS for individual H148 is: 14
N. of RUNS for individual H149 is: 15
N. of RUNS for individual H150 is: 17
N. of RUNS for individual H151 is: 18
N. of RUNS for individual H152 is: 13
N. of RUNS for individual H153 is: 17
N. of RUNS for individual H154 is: 21
N. of RUNS for individual H155 is: 16
You are using the method: CONSECUTIVE RUNS
Analysing Runs of Homozygosity (ROHom)
You are using the method: SLIDING WINDOWS
Analysing Runs of Heterozygosity (ROHet)
Window size: 10
Threshold for calling SNP in a Run: 0.05
N. of RUNS for individual H114 is: 17
N. of RUNS for individual H115 is: 15
N. of RUNS for individual H116 is: 22
N. of RUNS for individual H26 is: 25
N. of RUNS for individual H32 is: 27
N. of RUNS for individual H38 is: 37
N. of RUNS for individual H44 is: 26
N. of RUNS for individual H56 is: 30
N. of RUNS for individual H50 is: 16
N. of RUNS for individual H27 is: 23
N. of RUNS for individual H33 is: 27
N. of RUNS for individual H39 is: 23
N. of RUNS for individual H45 is: 28
N. of RUNS for individual H51 is: 25
N. of RUNS for individual H57 is: 19
N. of RUNS for individual H28 is: 29
N. of RUNS for individual H34 is: 26
N. of RUNS for individual H40 is: 22
N. of RUNS for individual H46 is: 24
N. of RUNS for individual H52 is: 26
N. of RUNS for individual H58 is: 19
N. of RUNS for individual H29 is: 19
N. of RUNS for individual H35 is: 17
N. of RUNS for individual H41 is: 22
N. of RUNS for individual H47 is: 26
N. of RUNS for individual H53 is: 26
N. of RUNS for individual H59 is: 32
N. of RUNS for individual H30 is: 36
N. of RUNS for individual H42 is: 30
N. of RUNS for individual H48 is: 26
N. of RUNS for individual H54 is: 22
N. of RUNS for individual H60 is: 22
N. of RUNS for individual H31 is: 27
N. of RUNS for individual H37 is: 29
N. of RUNS for individual H43 is: 24
N. of RUNS for individual H49 is: 21
N. of RUNS for individual H55 is: 21
N. of RUNS for individual H1 is: 21
N. of RUNS for individual H9 is: 17
N. of RUNS for individual H17 is: 18
N. of RUNS for individual H2 is: 29
N. of RUNS for individual H10 is: 24
N. of RUNS for individual H19 is: 29
N. of RUNS for individual H3 is: 23
N. of RUNS for individual H11 is: 31
N. of RUNS for individual H20 is: 16
N. of RUNS for individual H4 is: 27
N. of RUNS for individual H12 is: 19
N. of RUNS for individual H21 is: 12
N. of RUNS for individual H13 is: 17
N. of RUNS for individual H22 is: 20
N. of RUNS for individual H6 is: 24
N. of RUNS for individual H14 is: 28
N. of RUNS for individual H7 is: 23
N. of RUNS for individual H15 is: 28
N. of RUNS for individual H24 is: 37
N. of RUNS for individual H8 is: 27
N. of RUNS for individual H16 is: 18
N. of RUNS for individual H25 is: 24
N. of RUNS for individual H64 is: 14
N. of RUNS for individual H62 is: 31
N. of RUNS for individual H63 is: 37
N. of RUNS for individual H118 is: 19
N. of RUNS for individual H119 is: 21
N. of RUNS for individual H120 is: 17
N. of RUNS for individual H121 is: 22
N. of RUNS for individual H122 is: 26
N. of RUNS for individual H123 is: 21
N. of RUNS for individual H124 is: 26
N. of RUNS for individual H125 is: 21
N. of RUNS for individual H126 is: 19
N. of RUNS for individual H127 is: 23
N. of RUNS for individual H128 is: 26
N. of RUNS for individual H129 is: 9
N. of RUNS for individual H130 is: 21
N. of RUNS for individual H131 is: 21
N. of RUNS for individual H132 is: 24
N. of RUNS for individual H133 is: 21
N. of RUNS for individual H134 is: 17
N. of RUNS for individual H135 is: 24
N. of RUNS for individual H136 is: 23
N. of RUNS for individual H137 is: 21
N. of RUNS for individual H138 is: 22
N. of RUNS for individual H139 is: 26
N. of RUNS for individual H140 is: 20
N. of RUNS for individual H141 is: 16
N. of RUNS for individual H142 is: 22
N. of RUNS for individual H143 is: 24
N. of RUNS for individual H144 is: 20
N. of RUNS for individual H145 is: 19
N. of RUNS for individual H146 is: 20
N. of RUNS for individual H147 is: 14
N. of RUNS for individual H148 is: 20
N. of RUNS for individual H149 is: 22
N. of RUNS for individual H150 is: 21
N. of RUNS for individual H151 is: 23
N. of RUNS for individual H152 is: 25
N. of RUNS for individual H153 is: 22
N. of RUNS for individual H154 is: 19
N. of RUNS for individual H155 is: 20
You are using the method: CONSECUTIVE RUNS
Analysing Runs of Heterozygosity (ROHet)
Checking files...
Using class: 6
Total genome length: 290826950
calculating Froh on all genome
Total genome length: 290826950
calculating Froh chromosome by chromosome
Total genome length: 290826950
calculating Froh by Class
Class created: 0-6Class created: 6-12Class created: 12-24Class created: 24-48Class created: >48
Calculating SNPs inside ROH
Calculation % SNP in ROH
Chromosome founds:  2
Calculation % SNP in ROH finish
Quitting from lines 213-214 (detectRUNS.vignette.Rmd) 
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--- failed re-building ‘detectRUNS.vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘detectRUNS.vignette.Rmd’

Error: Vignette re-building failed.
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