############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/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 2024-12-25 18:27:05.227625 First, define topology of a map grid (2024-12-25 18:27:05.230199)... Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2024-12-25 18:27:05.230199)... Third, get training at the rough stage (2024-12-25 18:27:05.247664)... 1 out of 2 (2024-12-25 18:27:05.249549) updated (2024-12-25 18:27:05.271292) 2 out of 2 (2024-12-25 18:27:05.271707) updated (2024-12-25 18:27:05.298606) Fourth, get training at the finetune stage (2024-12-25 18:27:05.299085)... 1 out of 7 (2024-12-25 18:27:05.300735) updated (2024-12-25 18:27:05.325813) 2 out of 7 (2024-12-25 18:27:05.326198) updated (2024-12-25 18:27:05.364645) 3 out of 7 (2024-12-25 18:27:05.365038) updated (2024-12-25 18:27:05.389902) 4 out of 7 (2024-12-25 18:27:05.390349) updated (2024-12-25 18:27:05.413065) 5 out of 7 (2024-12-25 18:27:05.41344) updated (2024-12-25 18:27:05.445662) 6 out of 7 (2024-12-25 18:27:05.446036) updated (2024-12-25 18:27:05.466616) 7 out of 7 (2024-12-25 18:27:05.467134) updated (2024-12-25 18:27:05.489868) Next, identify the best-matching hexagon/rectangle for the input data (2024-12-25 18:27:05.490303)... Finally, append the response data (hits and mqe) into the sMap object (2024-12-25 18:27:05.513719)... 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: 2.02570726470381 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 2024-12-25 18:27:05.970782 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