############################################################################## ############################################################################## ### ### 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 2025-10-14 05:12:57.953635 First, define topology of a map grid (2025-10-14 05:12:57.954766)... Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-10-14 05:12:57.954766)... Third, get training at the rough stage (2025-10-14 05:12:57.975879)... 1 out of 2 (2025-10-14 05:12:57.9789) updated (2025-10-14 05:12:58.016473) 2 out of 2 (2025-10-14 05:12:58.017071) updated (2025-10-14 05:12:58.054258) Fourth, get training at the finetune stage (2025-10-14 05:12:58.054859)... 1 out of 7 (2025-10-14 05:12:58.056739) updated (2025-10-14 05:12:58.102328) 2 out of 7 (2025-10-14 05:12:58.102863) updated (2025-10-14 05:12:58.135512) 3 out of 7 (2025-10-14 05:12:58.136027) updated (2025-10-14 05:12:58.168785) 4 out of 7 (2025-10-14 05:12:58.169307) updated (2025-10-14 05:12:58.203352) 5 out of 7 (2025-10-14 05:12:58.203871) updated (2025-10-14 05:12:58.25305) 6 out of 7 (2025-10-14 05:12:58.253968) updated (2025-10-14 05:12:58.291381) 7 out of 7 (2025-10-14 05:12:58.291939) updated (2025-10-14 05:12:58.328467) Next, identify the best-matching hexagon/rectangle for the input data (2025-10-14 05:12:58.329146)... Finally, append the response data (hits and mqe) into the sMap object (2025-10-14 05:12:58.376181)... 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: 2.0634345450874 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 2025-10-14 05:12:58.993062 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