##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data supraHex
###
##############################################################################
##############################################################################


* 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
Warning in fun(libname, pkgname) :
  Package 'supraHex' is deprecated and will be removed from Bioconductor
  version 3.22
Start at 2025-01-28 02:48:15.246983

First, define topology of a map grid (2025-01-28 02:48:15.248115)...
Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-01-28 02:48:15.248115)...
Third, get training at the rough stage (2025-01-28 02:48:15.268755)...
	1 out of 2 (2025-01-28 02:48:15.271789)
	updated (2025-01-28 02:48:15.303915)
	2 out of 2 (2025-01-28 02:48:15.304466)
	updated (2025-01-28 02:48:15.335921)
Fourth, get training at the finetune stage (2025-01-28 02:48:15.336548)...
	1 out of 7 (2025-01-28 02:48:15.338439)
	updated (2025-01-28 02:48:15.370354)
	2 out of 7 (2025-01-28 02:48:15.37088)
	updated (2025-01-28 02:48:15.411007)
	3 out of 7 (2025-01-28 02:48:15.41155)
	updated (2025-01-28 02:48:15.439319)
	4 out of 7 (2025-01-28 02:48:15.439837)
	updated (2025-01-28 02:48:15.467947)
	5 out of 7 (2025-01-28 02:48:15.468475)
	updated (2025-01-28 02:48:15.507542)
	6 out of 7 (2025-01-28 02:48:15.508059)
	updated (2025-01-28 02:48:15.536238)
	7 out of 7 (2025-01-28 02:48:15.536796)
	updated (2025-01-28 02:48:15.574962)
Next, identify the best-matching hexagon/rectangle for the input data (2025-01-28 02:48:15.575909)...
Finally, append the response data (hits and mqe) into the sMap object (2025-01-28 02:48:15.606797)...

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: 2.0206725600483

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 2025-01-28 02:48:16.235872
Runtime in total is: 1 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