Error(s) in re-building vignettes:
  ...
--- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/AdvancedFeatures_files/figure-html/plot_codon-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12010 bytes
Input file size = 12100 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10399
  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 = 10399

Output IDAT size = 10399 bytes (1611 bytes decrease)
Output file size = 10477 bytes (1623 bytes = 13.41% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/AdvancedFeatures_files/figure-html/plot_codon-2.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12585 bytes
Input file size = 12675 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10861
  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 = 10861

Output IDAT size = 10861 bytes (1724 bytes decrease)
Output file size = 10939 bytes (1736 bytes = 13.70% decrease)

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

--- re-building ‘Ancestral.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Ancestral_files/figure-html/seqLogo-1.png
576x384 pixels, 8 bits/pixel, 242 colors in palette
Input IDAT size = 6538 bytes
Input file size = 7354 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5107
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5087
  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 = 5087

Output IDAT size = 5087 bytes (1451 bytes decrease)
Output file size = 5903 bytes (1451 bytes = 19.73% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Ancestral_files/figure-html/MPR-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31232 bytes
Input file size = 31346 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25338
  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 = 25338

Output IDAT size = 25338 bytes (5894 bytes decrease)
Output file size = 25416 bytes (5930 bytes = 18.92% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Ancestral_files/figure-html/plotML-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30026 bytes
Input file size = 30140 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24192
  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 = 24192

Output IDAT size = 24192 bytes (5834 bytes decrease)
Output file size = 24270 bytes (5870 bytes = 19.48% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Ancestral_files/figure-html/SYM_reconstruction-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 54620 bytes
Input file size = 54770 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 42445
  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 = 42445

Output IDAT size = 42445 bytes (12175 bytes decrease)
Output file size = 42523 bytes (12247 bytes = 22.36% decrease)

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

--- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-4-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 25362 bytes
Input file size = 26256 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 23473
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 22476
  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 = 22476

Output IDAT size = 22476 bytes (2886 bytes decrease)
Output file size = 22554 bytes (3702 bytes = 14.10% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-4-2.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18236 bytes
Input file size = 19118 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16887
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 16520
  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 = 16520

Output IDAT size = 16520 bytes (1716 bytes decrease)
Output file size = 16598 bytes (2520 bytes = 13.18% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-5-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 48391 bytes
Input file size = 48529 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 41071
  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 = 41071

Output IDAT size = 41071 bytes (7320 bytes decrease)
Output file size = 41149 bytes (7380 bytes = 15.21% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-6-1.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 43858 bytes
Input file size = 43996 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 38100
  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 = 38100

Output IDAT size = 38100 bytes (5758 bytes decrease)
Output file size = 38178 bytes (5818 bytes = 13.22% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-8-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 23039 bytes
Input file size = 23921 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21678
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 21384
  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 = 21384

Output IDAT size = 21384 bytes (1655 bytes decrease)
Output file size = 21462 bytes (2459 bytes = 10.28% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-9-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 19483 bytes
Input file size = 20365 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 18217
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 17688
  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 = 17688

Output IDAT size = 17688 bytes (1795 bytes decrease)
Output file size = 17766 bytes (2599 bytes = 12.76% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-9-2.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21561 bytes
Input file size = 22443 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20176
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 19896
  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 = 19896

Output IDAT size = 19896 bytes (1665 bytes decrease)
Output file size = 19974 bytes (2469 bytes = 11.00% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-9-3.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 53734 bytes
Input file size = 53884 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 45611
  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 = 45611

Output IDAT size = 45611 bytes (8123 bytes decrease)
Output file size = 45689 bytes (8195 bytes = 15.21% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-10-1.png
672x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25614 bytes
Input file size = 25728 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21099
  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 = 21099

Output IDAT size = 21099 bytes (4515 bytes decrease)
Output file size = 21177 bytes (4551 bytes = 17.69% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-12-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 12643 bytes
Input file size = 13513 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11094
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10871
  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 = 10871

Output IDAT size = 10871 bytes (1772 bytes decrease)
Output file size = 10949 bytes (2564 bytes = 18.97% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/IntertwiningTreesAndNetworks_files/figure-html/unnamed-chunk-13-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18720 bytes
Input file size = 19602 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17354
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 17015
  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 = 17015

Output IDAT size = 17015 bytes (1705 bytes decrease)
Output file size = 17093 bytes (2509 bytes = 12.80% decrease)

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

--- re-building ‘MLbyHand.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/MLbyHand_files/figure-html/plotBS-1.png
768x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10810 bytes
Input file size = 11680 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 9596
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 9278
  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 = 9278

Output IDAT size = 9278 bytes (1532 bytes decrease)
Output file size = 9356 bytes (2324 bytes = 19.90% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/MLbyHand_files/figure-html/ConsensusNet-1.png
768x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18008 bytes
Input file size = 18890 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16784
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 16220
  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 = 16220

Output IDAT size = 16220 bytes (1788 bytes decrease)
Output file size = 16298 bytes (2592 bytes = 13.72% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/MLbyHand_files/figure-html/allTrees-1.png
768x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 22151 bytes
Input file size = 23033 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20769
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 20719
  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 = 20719

Output IDAT size = 20719 bytes (1432 bytes decrease)
Output file size = 20797 bytes (2236 bytes = 9.71% decrease)

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

--- re-building ‘Morphological.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Morphological_files/figure-html/plot_cons_tree-1.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9344 bytes
Input file size = 10214 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8666
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 8434
  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 = 8434

Output IDAT size = 8434 bytes (910 bytes decrease)
Output file size = 8512 bytes (1702 bytes = 16.66% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Morphological_files/figure-html/plot_cons_tree-2.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9475 bytes
Input file size = 10345 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8858
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 8658
  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 = 8658

Output IDAT size = 8658 bytes (817 bytes decrease)
Output file size = 8736 bytes (1609 bytes = 15.55% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Morphological_files/figure-html/plot_cons_tree-3.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9265 bytes
Input file size = 10135 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8646
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 8448
  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 = 8448

Output IDAT size = 8448 bytes (817 bytes decrease)
Output file size = 8526 bytes (1609 bytes = 15.88% decrease)

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

--- re-building ‘Networx.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Networx_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3959 bytes
Input file size = 4814 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3439
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3329
  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 = 3329

Output IDAT size = 3329 bytes (630 bytes decrease)
Output file size = 3407 bytes (1407 bytes = 29.23% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Networx_files/figure-html/unnamed-chunk-2-2.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5614 bytes
Input file size = 6472 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5088
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 4968
  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 = 4968

Output IDAT size = 4968 bytes (646 bytes decrease)
Output file size = 5046 bytes (1426 bytes = 22.03% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Networx_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4214 bytes
Input file size = 5072 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3656
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3570
  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 = 3570

Output IDAT size = 3570 bytes (644 bytes decrease)
Output file size = 3648 bytes (1424 bytes = 28.08% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Networx_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5045 bytes
Input file size = 5903 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4457
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 4356
  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 = 4356

Output IDAT size = 4356 bytes (689 bytes decrease)
Output file size = 4434 bytes (1469 bytes = 24.89% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Networx_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4264 bytes
Input file size = 5119 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3648
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3523
  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 = 3523

Output IDAT size = 3523 bytes (741 bytes decrease)
Output file size = 3601 bytes (1518 bytes = 29.65% decrease)

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

--- re-building ‘Trees.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Trees_files/figure-html/plot1-1.png
768x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11413 bytes
Input file size = 12283 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10240
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 9904
  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 = 9904

Output IDAT size = 9904 bytes (1509 bytes decrease)
Output file size = 9982 bytes (2301 bytes = 18.73% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/vign_test/phangorn/vignettes/Trees_files/figure-html/plot2-1.png
768x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 13771 bytes
Input file size = 14641 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12542
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 12356
  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 = 12356

Output IDAT size = 12356 bytes (1415 bytes decrease)
Output file size = 12434 bytes (2207 bytes = 15.07% decrease)


Quitting from lines 64-66 [bootstrap_dist] (Trees.Rmd)
Error: processing vignette 'Trees.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 10)
--- failed re-building ‘Trees.Rmd’

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

Error: Vignette re-building failed.
Execution halted