Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Honeybee_biology.Rmd’ using rmarkdown
Killed
--- re-building ‘B_Multiple_colonies.Rmd’ using rmarkdown
--- finished re-building ‘B_Multiple_colonies.Rmd’

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

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

--- re-building ‘E_Genomics.Rmd’ using rmarkdown
SIMplyBee-package          package:SIMplyBee           R Documentation

_S_I_M_p_l_y_B_e_e: '_A_l_p_h_a_S_i_m_R' _E_x_t_e_n_s_i_o_n _f_o_r _S_i_m_u_l_a_t_i_n_g _H_o_n_e_y_b_e_e _P_o_p_u_l_a_t_i_o_n_s
_a_n_d _B_r_e_e_d_i_n_g _P_r_o_g_r_a_m_m_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     See the introductory vignette on using this package by running:
     'vignette("Honeybee_biology", package="SIMplyBee")'

_A_u_t_h_o_r(_s):

     *Maintainer*: Jana Obšteter <mailto:obsteter.jana@gmail.com>
     (ORCID)

     Authors:

        • Laura Strachan (ORCID)

        • Jernej Bubnič (ORCID)

        • Gregor Gorjanc (ORCID)

_S_e_e _A_l_s_o:

     Useful links:

        • <https://github.com/HighlanderLab/SIMplyBee>


** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/plot genoQ with poolW-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9029 bytes
Input file size = 9899 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8537
  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 = 8537

Output IDAT size = 8537 bytes (492 bytes decrease)
Output file size = 8615 bytes (1284 bytes = 12.97% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view diagonal-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27034 bytes
Input file size = 27148 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15876
  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 = 15876

Output IDAT size = 15876 bytes (11158 bytes decrease)
Output file size = 15954 bytes (11194 bytes = 41.23% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view diagonal-2.png
288x288 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3978 bytes
Input file size = 4827 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3540
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3524
  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 = 3524

Output IDAT size = 3524 bytes (454 bytes decrease)
Output file size = 3602 bytes (1225 bytes = 25.38% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4152 bytes
Input file size = 5007 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3681
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3680
  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 = 3680

Output IDAT size = 3680 bytes (472 bytes decrease)
Output file size = 3758 bytes (1249 bytes = 24.95% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs fathers 1-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5702 bytes
Input file size = 6560 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5301
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5299
  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 = 5299

Output IDAT size = 5299 bytes (403 bytes decrease)
Output file size = 5377 bytes (1183 bytes = 18.03% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs workers 1-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5920 bytes
Input file size = 6778 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5509
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5470
  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 = 5470

Output IDAT size = 5470 bytes (450 bytes decrease)
Output file size = 5548 bytes (1230 bytes = 18.15% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs drones 1-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5789 bytes
Input file size = 6647 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5351
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5314
  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 = 5314

Output IDAT size = 5314 bytes (475 bytes decrease)
Output file size = 5392 bytes (1255 bytes = 18.88% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/alleleFreq-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5399 bytes
Input file size = 6257 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5024
  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 = 5024

Output IDAT size = 5024 bytes (375 bytes decrease)
Output file size = 5102 bytes (1155 bytes = 18.46% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view calcGRMIbd-1.png
288x288 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11349 bytes
Input file size = 12213 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10831
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 10274
  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 = 10274

Output IDAT size = 10274 bytes (1075 bytes decrease)
Output file size = 10352 bytes (1861 bytes = 15.24% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view calcGRMIbd-2.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 13575 bytes
Input file size = 14442 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13144
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 13010
  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 = 13010

Output IDAT size = 13010 bytes (565 bytes decrease)
Output file size = 13088 bytes (1354 bytes = 9.38% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal1-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3872 bytes
Input file size = 4718 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3459
  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 = 3459

Output IDAT size = 3459 bytes (413 bytes decrease)
Output file size = 3537 bytes (1181 bytes = 25.03% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal1-2.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3867 bytes
Input file size = 4713 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3419
  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 = 3419

Output IDAT size = 3419 bytes (448 bytes decrease)
Output file size = 3497 bytes (1216 bytes = 25.80% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs fathers-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5336 bytes
Input file size = 6194 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4884
  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 = 4884

Output IDAT size = 4884 bytes (452 bytes decrease)
Output file size = 4962 bytes (1232 bytes = 19.89% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs workers-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5470 bytes
Input file size = 6328 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5046
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 5033
  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 = 5033

Output IDAT size = 5033 bytes (437 bytes decrease)
Output file size = 5111 bytes (1217 bytes = 19.23% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/Queen vs drones-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5338 bytes
Input file size = 6196 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4921
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 4920
  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 = 4920

Output IDAT size = 4920 bytes (418 bytes decrease)
Output file size = 4998 bytes (1198 bytes = 19.34% decrease)

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

--- re-building ‘G_Sampling_functions.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/G_Sampling_functions_files/figure-html/unnamed-chunk-3-1.png
576x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6617 bytes
Input file size = 7475 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5951
  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 = 5951

Output IDAT size = 5951 bytes (666 bytes decrease)
Output file size = 6029 bytes (1446 bytes = 19.34% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/G_Sampling_functions_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 = 4101 bytes
Input file size = 4956 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3650
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3649
  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 = 3649

Output IDAT size = 3649 bytes (452 bytes decrease)
Output file size = 3727 bytes (1229 bytes = 24.80% decrease)

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

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

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

Error: Vignette re-building failed.
Execution halted