Last updated on 2024-09-08 04:49:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.0 | 26.61 | 158.16 | 184.77 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.4.0 | 18.58 | 130.78 | 149.36 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.4.0 | 310.87 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.4.0 | 315.26 | OK | |||
| r-devel-windows-x86_64 | 0.4.0 | 32.00 | 218.00 | 250.00 | OK | |
| r-patched-linux-x86_64 | 0.4.0 | 29.03 | 160.73 | 189.76 | OK | |
| r-release-linux-x86_64 | 0.4.0 | 25.95 | 157.88 | 183.83 | ERROR | |
| r-release-macos-arm64 | 0.4.0 | 105.00 | OK | |||
| r-release-macos-x86_64 | 0.4.0 | 189.00 | OK | |||
| r-release-windows-x86_64 | 0.4.0 | 31.00 | 210.00 | 241.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.0 | 144.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.4.0 | 214.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.4.0 | 39.00 | 262.00 | 301.00 | OK |
Version: 0.4.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A_Honeybee_biology.Rmd’ using rmarkdown
--- finished re-building ‘A_Honeybee_biology.Rmd’
--- 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
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/D_Crossing_files/figure-html/unnamed-chunk-12-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10598 bytes
Input file size = 10688 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8078
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 = 8078
Output IDAT size = 8078 bytes (2520 bytes decrease)
Output file size = 8156 bytes (2532 bytes = 23.69% decrease)
Quitting from lines 387-403 [unnamed-chunk-16] (D_Crossing.Rmd)
Error: processing vignette 'D_Crossing.Rmd' failed with diagnostics:
Missing queen!
--- failed re-building ‘D_Crossing.Rmd’
--- re-building ‘E_Genomics.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-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 = 9395 bytes
Input file size = 10265 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8893
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 8874
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 = 8874
Output IDAT size = 8874 bytes (521 bytes decrease)
Output file size = 8952 bytes (1313 bytes = 12.79% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 27984 bytes
Input file size = 28098 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16785
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 = 16785
Output IDAT size = 16785 bytes (11199 bytes decrease)
Output file size = 16863 bytes (11235 bytes = 39.99% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view diagonal-2.png
288x288 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4242 bytes
Input file size = 5094 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3742
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3735
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 = 3735
Output IDAT size = 3735 bytes (507 bytes decrease)
Output file size = 3813 bytes (1281 bytes = 25.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3890 bytes
Input file size = 4736 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3450
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3437
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 = 3437
Output IDAT size = 3437 bytes (453 bytes decrease)
Output file size = 3515 bytes (1221 bytes = 25.78% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 5842 bytes
Input file size = 6700 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5436
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5425
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 = 5425
Output IDAT size = 5425 bytes (417 bytes decrease)
Output file size = 5503 bytes (1197 bytes = 17.87% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 6076 bytes
Input file size = 6934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5628
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5595
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 = 5595
Output IDAT size = 5595 bytes (481 bytes decrease)
Output file size = 5673 bytes (1261 bytes = 18.19% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 6200 bytes
Input file size = 7058 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5731
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5699
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 = 5699
Output IDAT size = 5699 bytes (501 bytes decrease)
Output file size = 5777 bytes (1281 bytes = 18.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 5632 bytes
Input file size = 6490 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5216
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 = 5216
Output IDAT size = 5216 bytes (416 bytes decrease)
Output file size = 5294 bytes (1196 bytes = 18.43% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 11340 bytes
Input file size = 12204 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10814
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 10266
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 = 10266
Output IDAT size = 10266 bytes (1074 bytes decrease)
Output file size = 10344 bytes (1860 bytes = 15.24% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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 = 13549 bytes
Input file size = 14416 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13136
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 12994
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 = 12994
Output IDAT size = 12994 bytes (555 bytes decrease)
Output file size = 13072 bytes (1344 bytes = 9.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal1-1.png
288x288 pixels, 8 bits/pixel, 251 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3899 bytes
Input file size = 4742 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3470
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 = 3470
Output IDAT size = 3470 bytes (429 bytes decrease)
Output file size = 3548 bytes (1194 bytes = 25.18% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/E_Genomics_files/figure-html/view non-diagonal1-2.png
288x288 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3810 bytes
Input file size = 4659 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3369
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 = 3369
Output IDAT size = 3369 bytes (441 bytes decrease)
Output file size = 3447 bytes (1212 bytes = 26.01% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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-release-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-release-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 ‘F_Quantitative_Genetics.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/basePop_virgin_queens-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11914 bytes
Input file size = 12784 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10870
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 = 10870
Output IDAT size = 10870 bytes (1044 bytes decrease)
Output file size = 10948 bytes (1836 bytes = 14.36% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/basePop_drones-1.png
480x259 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6006 bytes
Input file size = 6864 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5508
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 (536 bytes decrease)
Output file size = 5548 bytes (1316 bytes = 19.17% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/plot_queen_vs_worker_values-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8463 bytes
Input file size = 9333 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7707
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 = 7707
Output IDAT size = 7707 bytes (756 bytes decrease)
Output file size = 7785 bytes (1548 bytes = 16.59% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/distribution_by_patriline-1.png
576x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 89921 bytes
Input file size = 90119 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 74003
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 = 74003
Output IDAT size = 74003 bytes (15918 bytes decrease)
Output file size = 74081 bytes (16038 bytes = 17.80% decrease)
calcColonyValue package:SIMplyBee R Documentation
_<08>C_<08>a_<08>l_<08>c_<08>u_<08>l_<08>a_<08>t_<08>e _<08>c_<08>o_<08>l_<08>o_<08>n_<08>y _<08>v_<08>a_<08>l_<08>u_<08>e(_<08>s)
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Level 0 function that calculate value(s) of a colony.
_<08>U_<08>s_<08>a_<08>g_<08>e:
calcColonyValue(x, FUN = NULL, simParamBee = NULL, ...)
calcColonyPheno(x, FUN = mapCasteToColonyPheno, simParamBee = NULL, ...)
calcColonyGv(x, FUN = mapCasteToColonyGv, simParamBee = NULL, ...)
calcColonyBv(x, FUN = mapCasteToColonyBv, simParamBee = NULL, ...)
calcColonyDd(x, FUN = mapCasteToColonyDd, simParamBee = NULL, ...)
calcColonyAa(x, FUN = mapCasteToColonyAa, simParamBee = NULL, ...)
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
x: 'Colony-class' or 'MultiColony-class'
FUN: function, that calculates colony value from values of colony
members
simParamBee: 'SimParamBee', global simulation parameters
...: other arguments of 'FUN'
_<08>V_<08>a_<08>l_<08>u_<08>e:
a matrix with one value or a row of values when 'x' is
'Colony-class' and a row-named matrix when 'x' is
'MultiColony-class', where names are colony IDs
_<08>F_<08>u_<08>n_<08>c_<08>t_<08>i_<08>o_<08>n_<08>s:
• 'calcColonyPheno()': Calculate colony phenotype value from
caste individuals' phenotype values
• 'calcColonyGv()': Calculate colony genetic value from caste
individuals' genetic values
• 'calcColonyBv()': Calculate colony breeding value from caste
individuals' breeding values
• 'calcColonyDd()': Calculate colony dominance value from caste
individuals' dominance values
• 'calcColonyAa()': Calculate colony epistasis value from caste
individuals' epistasis value
_<08>S_<08>e_<08>e _<08>A_<08>l_<08>s_<08>o:
'mapCasteToColonyValue' as an example of 'FUN', 'selectColonies'
for example for to select colonies based on these values, and
'vignette(topic = "QuantitativeGenetics", package = "SIMplyBee")'
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
# Define two traits that collectively affect colony honey yield:
# 1) queen's effect on colony honey yield, say via pheromone secretion phenotype
# 2) workers' effect on colony honey yield, say via foraging ability phenotype
# The traits will have a negative genetic correlation of -0.5 and heritability
# of 0.25 (on an individual level)
nWorkers <- 10
mean <- c(10, 10 / nWorkers)
varA <- c(1, 1 / nWorkers)
corA <- matrix(data = c(
1.0, -0.5,
-0.5, 1.0
), nrow = 2, byrow = TRUE)
varE <- c(3, 3 / nWorkers)
varA / (varA + varE)
SP$addTraitADE(nQtlPerChr = 100,
mean = mean,
var = varA, corA = corA,
meanDD = 0.1, varDD = 0.2, corD = corA,
relAA = 0.1, corAA = corA)
SP$setVarE(varE = varE)
basePop <- createVirginQueens(founderGenomes)
drones <- createDrones(x = basePop[1], nInd = 200)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
# Create and cross Colony and MultiColony class
colony <- createColony(x = basePop[2])
colony <- cross(colony, drones = droneGroups[[1]])
colony <- buildUp(colony, nWorkers = nWorkers, nDrones = 3)
apiary <- createMultiColony(basePop[3:5], n = 2)
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
apiary <- buildUp(apiary, nWorkers = nWorkers, nDrones = 3)
# Colony value - shorthand version
# (using the default mapCasteToColony*() functions - you can provide yours instead!)
# Phenotype value
calcColonyPheno(colony)
calcColonyPheno(apiary)
# Genetic value
calcColonyGv(colony)
calcColonyGv(apiary)
# Colony value - long version
# (using the default mapCasteToColony*() function - you can provide yours instead!)
calcColonyValue(colony, FUN = mapCasteToColonyPheno)
calcColonyValue(apiary, FUN = mapCasteToColonyPheno)
# Colony value - long version - using a function stored in SimParamBee (SP)
# (using the default mapCasteToColony*() function - you can provide yours instead!)
SP$colonyValueFUN <- mapCasteToColonyPheno
calcColonyValue(colony)
calcColonyValue(apiary)
mapCasteToColonyValue package:SIMplyBee R Documentation
_<08>M_<08>a_<08>p _<08>c_<08>a_<08>s_<08>t_<08>e _<08>m_<08>e_<08>m_<08>b_<08>e_<08>r (_<08>i_<08>n_<08>d_<08>i_<08>v_<08>i_<08>d_<08>u_<08>a_<08>l) _<08>v_<08>a_<08>l_<08>u_<08>e_<08>s _<08>t_<08>o _<08>a _<08>c_<08>o_<08>l_<08>o_<08>n_<08>y _<08>v_<08>a_<08>l_<08>u_<08>e
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Maps caste member (individual) values to a colony value - for
phenotype, genetic, breeding, dominance, and epistasis values.
This function can be used as 'FUN' argument in 'calcColonyValue'
function(s). It can also be saved in 'SimParamBee$colonyValueFUN'
as a default function called by 'calcColonyValue' function(s).
This is just an example - quite a flexible one! You can provide
your own "caste functions" that satisfy your needs within this
mapping function (see 'queenFUN', 'workersFUN', and 'dronesFUN'
below) or provide a complete replacement of this mapping function!
For example, this mapping function does not cater for indirect
(social) genetic effects where colony individuals value impacts
value of other colony individuals. Note though that you can
achieve this impact also via multiple correlated traits, such as a
queen and a workers trait.
_<08>U_<08>s_<08>a_<08>g_<08>e:
mapCasteToColonyValue(
colony,
value = "pheno",
queenTrait = 1,
queenFUN = function(x) x,
workersTrait = 2,
workersFUN = colSums,
dronesTrait = NULL,
dronesFUN = NULL,
traitName = NULL,
combineFUN = function(q, w, d) q + w,
checkProduction = TRUE,
notProductiveValue = 0,
simParamBee = NULL
)
mapCasteToColonyPheno(colony, simParamBee = NULL, ...)
mapCasteToColonyGv(colony, simParamBee = NULL, ...)
mapCasteToColonyBv(colony, simParamBee = NULL, ...)
mapCasteToColonyDd(colony, simParamBee = NULL, ...)
mapCasteToColonyAa(colony, simParamBee = NULL, ...)
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
colony: 'Colony-class'
value: character, one of 'pheno' or 'gv'
queenTrait: numeric (column position) or character (column name),
trait(s) that represents queen's contribution to colony
value(s); if 'NULL' then this contribution is 0; you can pass
more than one trait here, but make sure that 'combineFUN'
works with these trait dimensions
queenFUN: function, function that will be applied to queen's value
workersTrait: numeric (column position) or character (column name),
trait(s) that represents workers' contribution to colony
value(s); if 'NULL' then this contribution is 0; you can pass
more than one trait here, but make sure that 'combineFUN'
works with these trait dimensions
workersFUN: function, function that will be applied to workers values
dronesTrait: numeric (column position) or character (column name),
trait(s) that represents drones' contribution to colony
value(s); if 'NULL' then this contribution is 0; you can pass
more than one trait here, but make sure that 'combineFUN'
works with these trait dimensions
dronesFUN: function, function that will be applied to drone values
traitName: the name of the colony trait(s), say, honeyYield; you can
pass more than one trait name here, but make sure to match
them with 'combineFUN' trait dimensions
combineFUN: function that will combine the queen, worker, and drone
contributions - this function should be defined as
'function(q, w, d)' where 'q' represents queen's, 'q'
represents workers', and 'd' represents drones' contribution.
checkProduction: logical, does the value depend on the production
status of colony; if yes and production is 'FALSE', the
return is 'notProductiveValue' - this will often make sense
for colony phenotype value only; you can pass more than one
logical value here (one per trait coming out of 'combineFUN')
notProductiveValue: numeric, returned value when colony is not
productive; you can pass more than one logical value here
(one per trait coming out of 'combineFUN')
simParamBee: 'SimParamBee', global simulation parameters
...: other arguments of 'mapCasteToColonyValue' (for its aliases)
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
This is a utility/mapping function meant to be called by
'calcColonyValue'. It only works on a single colony - use
'calcColonyValue' to get Colony or MultiColony values.
_<08>V_<08>a_<08>l_<08>u_<08>e:
numeric matrix with one value or a row of values
_<08>F_<08>u_<08>n_<08>c_<08>t_<08>i_<08>o_<08>n_<08>s:
• 'mapCasteToColonyPheno()': Map caste member (individual)
phenotype values to a colony phenotype value
• 'mapCasteToColonyGv()': Map caste member (individual) genetic
values to a colony genetic value
• 'mapCasteToColonyBv()': Map caste member (individual)
breeding values to a colony breeding value
• 'mapCasteToColonyDd()': Map caste member (individual)
dominance values to a colony dominance value
• 'mapCasteToColonyAa()': Map caste member (individual)
epistasis values to a colony epistasis value
_<08>S_<08>e_<08>e _<08>A_<08>l_<08>s_<08>o:
'SimParamBee' field 'colonyValueFUN' and functions
'calcColonyValue', 'calcColonyPheno', 'calcColonyGv', 'getEvents',
'pheno', and 'gv', as well as 'vignette(topic =
"QuantitativeGenetics", package = "SIMplyBee")'
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
# Define two traits that collectively affect colony honey yield:
# 1) queen's effect on colony honey yield, say via pheromone secretion phenotype
# 2) workers' effect on colony honey yield, say via foraging ability phenotype
# The traits will have a negative genetic correlation of -0.5 and heritability
# of 0.25 (on an individual level)
nWorkers <- 10
mean <- c(10, 10 / nWorkers)
varA <- c(1, 1 / nWorkers)
corA <- matrix(data = c(
1.0, -0.5,
-0.5, 1.0
), nrow = 2, byrow = TRUE)
varE <- c(3, 3 / nWorkers)
varA / (varA + varE)
SP$addTraitADE(nQtlPerChr = 100,
mean = mean,
var = varA, corA = corA,
meanDD = 0.1, varDD = 0.2, corD = corA,
relAA = 0.1, corAA = corA)
SP$setVarE(varE = varE)
basePop <- createVirginQueens(founderGenomes)
drones <- createDrones(x = basePop[1], nInd = 10)
colony <- createColony(x = basePop[2])
colony <- cross(colony, drones = drones)
colony <- buildUp(colony, nWorkers = nWorkers, nDrones = 3)
# Colony value
mapCasteToColonyPheno(colony)
mapCasteToColonyGv(colony)
# To understand where the above values come from, study the contents of
# mapCasteToColonyValue() and the values below:
# Phenotype values
getQueenPheno(colony)
getWorkersPheno(colony)
# Genetic values
getQueenGv(colony)
getWorkersGv(colony)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/queen_values-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 13362 bytes
Input file size = 14232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11654
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 = 11654
Output IDAT size = 11654 bytes (1708 bytes decrease)
Output file size = 11732 bytes (2500 bytes = 17.57% decrease)
nWorkersPoisson package:SIMplyBee R Documentation
_<08>S_<08>a_<08>m_<08>p_<08>l_<08>e _<08>a _<08>n_<08>u_<08>m_<08>b_<08>e_<08>r _<08>o_<08>f _<08>w_<08>o_<08>r_<08>k_<08>e_<08>r_<08>s
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Sample a number of workers - used when 'nInd = NULL' (see
'SimParamBee$nWorkers').
This is just an example. You can provide your own functions that
satisfy your needs!
_<08>U_<08>s_<08>a_<08>g_<08>e:
nWorkersPoisson(colony, n = 1, average = 100)
nWorkersTruncPoisson(colony, n = 1, average = 100, lowerLimit = 0)
nWorkersColonyPhenotype(
colony,
queenTrait = 1,
workersTrait = NULL,
checkProduction = FALSE,
lowerLimit = 0,
simParamBee = NULL,
...
)
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
colony: 'Colony-class'
n: integer, number of samples
average: numeric, average number of workers
lowerLimit: numeric, returned numbers will be above this value
queenTrait: numeric (column position) or character (column name), trait
that represents queen's effect on the colony phenotype
(defined in 'SimParamBee' - see examples); if '0' then this
effect is 0
workersTrait: numeric (column position) or character (column name),
trait that represents workers's effect on the colony
phenotype (defined in 'SimParamBee' - see examples); if '0'
then this effect is 0
checkProduction: logical, does the phenotype depend on the production
status of colony; if yes and production is not 'TRUE', the
result is above 'lowerLimit'
simParamBee: 'SimParamBee', global simulation parameters
...: other arguments of 'mapCasteToColonyPheno'
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
'nWorkersPoisson' samples from a Poisson distribution with a given
average, which can return a value 0. 'nDronesTruncPoisson' samples
from a zero truncated Poisson distribution.
'nWorkersColonyPhenotype' returns a number (above 'lowerLimit') as
a function of colony phenotype, say queen's fecundity. Colony
phenotype is provided by 'mapCasteToColonyPheno'. You need to set
up traits influencing the colony phenotype and their parameters
(mean and variances) via 'SimParamBee' (see examples).
_<08>V_<08>a_<08>l_<08>u_<08>e:
numeric, number of workers
_<08>F_<08>u_<08>n_<08>c_<08>t_<08>i_<08>o_<08>n_<08>s:
• 'nWorkersTruncPoisson()': Sample a non-zero number of workers
• 'nWorkersColonyPhenotype()': Sample a non-zero number of
workers based on colony phenotype, say queen's fecundity
_<08>S_<08>e_<08>e _<08>A_<08>l_<08>s_<08>o:
'SimParamBee' field 'nWorkers' and 'vignette(topic =
"QuantitativeGenetics", package = "SIMplyBee")'
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
nWorkersPoisson()
nWorkersPoisson()
n <- nWorkersPoisson(n = 1000)
hist(n, breaks = seq(from = min(n), to = max(n)), xlim = c(0, 200))
table(n)
nWorkersTruncPoisson()
nWorkersTruncPoisson()
n <- nWorkersTruncPoisson(n = 1000)
hist(n, breaks = seq(from = min(n), to = max(n)), xlim = c(0, 200))
table(n)
# Example for nWorkersColonyPhenotype()
founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
average <- 100
h2 <- 0.1
SP$addTraitA(nQtlPerChr = 100, mean = average, var = average * h2)
SP$setVarE(varE = average * (1 - h2))
basePop <- createVirginQueens(founderGenomes)
drones <- createDrones(x = basePop[1], nInd = 50)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 2, nDrones = 15)
colony1 <- createColony(x = basePop[2])
colony2 <- createColony(x = basePop[3])
colony1 <- cross(colony1, drones = droneGroups[[1]])
colony2 <- cross(colony2, drones = droneGroups[[2]])
colony1@queen@pheno
colony2@queen@pheno
createWorkers(colony1, nInd = nWorkersColonyPhenotype)
createWorkers(colony2, nInd = nWorkersColonyPhenotype)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SIMplyBee.Rcheck/vign_test/SIMplyBee/vignettes/F_Quantitative_Genetics_files/figure-html/colony_pheno_3-1.png
624x528 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 24856 bytes
Input file size = 25750 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22146
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 22127
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 = 22127
Output IDAT size = 22127 bytes (2729 bytes decrease)
Output file size = 22205 bytes (3545 bytes = 13.77% decrease)
--- finished re-building ‘F_Quantitative_Genetics.Rmd’
--- re-building ‘G_Sampling_functions.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-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 = 6392 bytes
Input file size = 7250 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5811
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 = 5811
Output IDAT size = 5811 bytes (581 bytes decrease)
Output file size = 5889 bytes (1361 bytes = 18.77% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-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, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4114 bytes
Input file size = 4972 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3640
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3635
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 = 3635
Output IDAT size = 3635 bytes (479 bytes decrease)
Output file size = 3713 bytes (1259 bytes = 25.32% 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:
‘D_Crossing.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64