Last updated on 2024-06-15 01:51:45 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| SIMplyBee | 1 | 9 | 3 |
Current CRAN status: ERROR: 1, NOTE: 9, OK: 3
Version: 0.3.0
Check: Rd files
Result: NOTE
checkRd: (-1) cross.Rd:11: Lost braces
11 | \item{x}{\code{\link{Pop-class}} or code{\link{Colony-class}} or \code{\link{MultiColony-class}},
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR
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
_<08>S_<08>I_<08>M_<08>p_<08>l_<08>y_<08>B_<08>e_<08>e: '_<08>A_<08>l_<08>p_<08>h_<08>a_<08>S_<08>i_<08>m_<08>R' _<08>E_<08>x_<08>t_<08>e_<08>n_<08>s_<08>i_<08>o_<08>n _<08>f_<08>o_<08>r _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>n_<08>g _<08>H_<08>o_<08>n_<08>e_<08>y_<08>b_<08>e_<08>e _<08>P_<08>o_<08>p_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s
_<08>a_<08>n_<08>d _<08>B_<08>r_<08>e_<08>e_<08>d_<08>i_<08>n_<08>g _<08>P_<08>r_<08>o_<08>g_<08>r_<08>a_<08>m_<08>m_<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:
See the introductory vignette on using this package by running:
'vignette("Honeybee_biology", package="SIMplyBee")'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
*Maintainer*: Jana Obšteter <mailto:obsteter.jana@gmail.com>
(ORCID)
Authors:
• Laura Strachan (ORCID)
• Jernej Bubnič (ORCID)
• Gregor Gorjanc (ORCID)
_<08>S_<08>e_<08>e _<08>A_<08>l_<08>s_<08>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
Flavor: r-devel-linux-x86_64-debian-gcc