Error(s) in re-building vignettes:
  ...
--- re-building ‘HCP_analysis.Rmd’ using rmarkdown

Quitting from lines 55-60 [unnamed-chunk-2] (HCP_analysis.Rmd)
Error: processing vignette 'HCP_analysis.Rmd' failed with diagnostics:
Package "igraph" must be installed to use this function.
--- failed re-building ‘HCP_analysis.Rmd’

--- re-building ‘ML_and_Inference.Rmd’ using rmarkdown
Loading required namespace: TDAstats
Failed with error:  'there is no package called 'TDAstats''
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-4-1.png
768x768 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 16621 bytes
Input file size = 17503 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14986
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 14882
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 14882

Output IDAT size = 14882 bytes (1739 bytes decrease)
Output file size = 14960 bytes (2543 bytes = 14.53% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-11-1.png
1344x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 22132 bytes
Input file size = 22234 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18978
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18978

Output IDAT size = 18978 bytes (3154 bytes decrease)
Output file size = 19056 bytes (3178 bytes = 14.29% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-12-1.png
960x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11790 bytes
Input file size = 12660 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10065
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10065

Output IDAT size = 10065 bytes (1725 bytes decrease)
Output file size = 10143 bytes (2517 bytes = 19.88% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-13-1.png
1344x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44956 bytes
Input file size = 45094 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 37171
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 37003
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 37003

Output IDAT size = 37003 bytes (7953 bytes decrease)
Output file size = 37081 bytes (8013 bytes = 17.77% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-21-1.png
960x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42770 bytes
Input file size = 42908 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 34590
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 34590

Output IDAT size = 34590 bytes (8180 bytes decrease)
Output file size = 34668 bytes (8240 bytes = 19.20% decrease)

Loading required namespace: TDAstats
Failed with error:  'there is no package called 'TDAstats''
Loading required namespace: TDA
Failed with error:  'there is no package called 'TDA''
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-24-1.png
1536x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 55127 bytes
Input file size = 55277 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 47136
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 47136

Output IDAT size = 47136 bytes (7991 bytes decrease)
Output file size = 47214 bytes (8063 bytes = 14.59% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-33-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 104971 bytes
Input file size = 105193 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 85080
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 85080

Output IDAT size = 85080 bytes (19891 bytes decrease)
Output file size = 85158 bytes (20035 bytes = 19.05% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-34-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 52384 bytes
Input file size = 52534 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 39337
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 39337

Output IDAT size = 39337 bytes (13047 bytes decrease)
Output file size = 39415 bytes (13119 bytes = 24.97% decrease)

Loading required namespace: igraph
Failed with error:  'there is no package called 'igraph''
Loading required namespace: igraph
Failed with error:  'there is no package called 'igraph''
Loading required namespace: igraph
Failed with error:  'there is no package called 'igraph''
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-39-1.png
1344x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 22132 bytes
Input file size = 22234 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18978
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18978

Output IDAT size = 18978 bytes (3154 bytes decrease)
Output file size = 19056 bytes (3178 bytes = 14.29% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-42-1.png
960x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 33146 bytes
Input file size = 33272 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26706
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 26686
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 26686

Output IDAT size = 26686 bytes (6460 bytes decrease)
Output file size = 26764 bytes (6508 bytes = 19.56% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-47-1.png
1152x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38260 bytes
Input file size = 38386 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30429
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30429

Output IDAT size = 30429 bytes (7831 bytes decrease)
Output file size = 30507 bytes (7879 bytes = 20.53% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-48-1.png
1152x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38058 bytes
Input file size = 38184 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 29842
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 29842

Output IDAT size = 29842 bytes (8216 bytes decrease)
Output file size = 29920 bytes (8264 bytes = 21.64% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/ML_and_Inference_files/figure-html/unnamed-chunk-49-1.png
1152x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37934 bytes
Input file size = 38060 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30152
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30152

Output IDAT size = 30152 bytes (7782 bytes decrease)
Output file size = 30230 bytes (7830 bytes = 20.57% decrease)

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

--- re-building ‘Speed.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/Speed_files/figure-html/unnamed-chunk-2-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 57813 bytes
Input file size = 57975 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 44586
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 44586

Output IDAT size = 44586 bytes (13227 bytes decrease)
Output file size = 44664 bytes (13311 bytes = 22.96% decrease)

Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/Speed_files/figure-html/unnamed-chunk-9-1.png
1344x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 103383 bytes
Input file size = 103605 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 84514
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 84514

Output IDAT size = 84514 bytes (18869 bytes decrease)
Output file size = 84592 bytes (19013 bytes = 18.35% decrease)

Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/Speed_files/figure-html/unnamed-chunk-11-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49314 bytes
Input file size = 49464 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 38869
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 38869

Output IDAT size = 38869 bytes (10445 bytes decrease)
Output file size = 38947 bytes (10517 bytes = 21.26% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/Speed_files/figure-html/unnamed-chunk-13-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46931 bytes
Input file size = 47069 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36790
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36790

Output IDAT size = 36790 bytes (10141 bytes decrease)
Output file size = 36868 bytes (10201 bytes = 21.67% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/Speed_files/figure-html/unnamed-chunk-15-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 53007 bytes
Input file size = 53157 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 41308
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 41308

Output IDAT size = 41308 bytes (11699 bytes decrease)
Output file size = 41386 bytes (11771 bytes = 22.14% decrease)

--- finished re-building ‘Speed.Rmd’

--- re-building ‘comparing_calcs.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDApplied.Rcheck/vign_test/TDApplied/vignettes/comparing_calcs_files/figure-html/unnamed-chunk-2-1.png
1344x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 22132 bytes
Input file size = 22234 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18978
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18978

Output IDAT size = 18978 bytes (3154 bytes decrease)
Output file size = 19056 bytes (3178 bytes = 14.29% decrease)

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

--- re-building ‘personalized_analyses.Rmd’ using rmarkdown
--- finished re-building ‘personalized_analyses.Rmd’

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

Error: Vignette re-building failed.
Execution halted