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### Running command:
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###   chmod a+r supraHex -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data supraHex
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* checking for file 'supraHex/DESCRIPTION' ... OK
* preparing 'supraHex':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'supraHex_vignettes.Rnw' using Sweave
Loading required package: hexbin
Start at 2025-01-27 22:17:30.017629

First, define topology of a map grid (2025-01-27 22:17:30.01953)...
Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-01-27 22:17:30.01953)...
Third, get training at the rough stage (2025-01-27 22:17:30.035975)...
	1 out of 2 (2025-01-27 22:17:30.038151)
	updated (2025-01-27 22:17:30.064308)
	2 out of 2 (2025-01-27 22:17:30.064871)
	updated (2025-01-27 22:17:30.090826)
Fourth, get training at the finetune stage (2025-01-27 22:17:30.091422)...
	1 out of 7 (2025-01-27 22:17:30.092945)
	updated (2025-01-27 22:17:30.143537)
	2 out of 7 (2025-01-27 22:17:30.145585)
	updated (2025-01-27 22:17:30.176296)
	3 out of 7 (2025-01-27 22:17:30.176792)
	updated (2025-01-27 22:17:30.205904)
	4 out of 7 (2025-01-27 22:17:30.206413)
	updated (2025-01-27 22:17:30.23186)
	5 out of 7 (2025-01-27 22:17:30.232344)
	updated (2025-01-27 22:17:30.269946)
	6 out of 7 (2025-01-27 22:17:30.270429)
	updated (2025-01-27 22:17:30.294577)
	7 out of 7 (2025-01-27 22:17:30.295057)
	updated (2025-01-27 22:17:30.31993)
Next, identify the best-matching hexagon/rectangle for the input data (2025-01-27 22:17:30.32045)...
Finally, append the response data (hits and mqe) into the sMap object (2025-01-27 22:17:30.342409)...

Below are the summaries of the training results:
   dimension of input data: 1000x6
   xy-dimension of map grid: xdim=15, ydim=15, r=8
   grid lattice: hexa
   grid shape: suprahex
   dimension of grid coord: 169x2
   initialisation method: linear
   dimension of codebook matrix: 169x6
   mean quantization error: 2.01314814562829

Below are the details of trainology:
   training algorithm: batch
   alpha type: invert
   training neighborhood kernel: gaussian
   trainlength (x input data length): 2 at rough stage; 7 at finetune stage
   radius (at rough stage): from 4 to 1
   radius (at finetune stage): from 1 to 1

End at 2025-01-27 22:17:30.769639
Runtime in total is: 0 secs

Warning: The `path` argument of `write_delim()` is deprecated as of readr 1.4.0.
ℹ Please use the `file` argument instead.
ℹ The deprecated feature was likely used in the supraHex package.
  Please report the issue to the authors.

Error: processing vignette 'supraHex_vignettes.Rnw' failed with diagnostics:
 chunk 18 
Error in igraph::as_data_frame(., what = "edge") : 
  `arg` must be one of "edges", "vertices", or "both", not "edge".
ℹ Did you mean "edges"?

--- failed re-building 'supraHex_vignettes.Rnw'

SUMMARY: processing the following file failed:
  'supraHex_vignettes.Rnw'

Error: Vignette re-building failed.
Execution halted