############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/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 2025-03-06 13:33:02.53108 First, define topology of a map grid (2025-03-06 13:33:02.53177)... Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-03-06 13:33:02.53177)... Third, get training at the rough stage (2025-03-06 13:33:02.543173)... 1 out of 2 (2025-03-06 13:33:02.544848) updated (2025-03-06 13:33:02.563769) 2 out of 2 (2025-03-06 13:33:02.564028) updated (2025-03-06 13:33:02.582881) Fourth, get training at the finetune stage (2025-03-06 13:33:02.583159)... 1 out of 7 (2025-03-06 13:33:02.584248) updated (2025-03-06 13:33:02.604872) 2 out of 7 (2025-03-06 13:33:02.605089) updated (2025-03-06 13:33:02.616161) 3 out of 7 (2025-03-06 13:33:02.616369) updated (2025-03-06 13:33:02.631005) 4 out of 7 (2025-03-06 13:33:02.631215) updated (2025-03-06 13:33:02.646299) 5 out of 7 (2025-03-06 13:33:02.646554) updated (2025-03-06 13:33:02.66447) 6 out of 7 (2025-03-06 13:33:02.664744) updated (2025-03-06 13:33:02.675765) 7 out of 7 (2025-03-06 13:33:02.675972) updated (2025-03-06 13:33:02.686936) Next, identify the best-matching hexagon/rectangle for the input data (2025-03-06 13:33:02.687177)... Finally, append the response data (hits and mqe) into the sMap object (2025-03-06 13:33:02.697827)... 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: 1.97075108170617 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 2025-03-06 13:33:03.001177 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