############################################################################## ############################################################################## ### ### 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 2025-02-03 13:32:39.06302 First, define topology of a map grid (2025-02-03 13:32:39.063721)... Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-02-03 13:32:39.063721)... Third, get training at the rough stage (2025-02-03 13:32:39.075609)... 1 out of 2 (2025-02-03 13:32:39.07759) updated (2025-02-03 13:32:39.098885) 2 out of 2 (2025-02-03 13:32:39.099158) updated (2025-02-03 13:32:39.119718) Fourth, get training at the finetune stage (2025-02-03 13:32:39.119999)... 1 out of 7 (2025-02-03 13:32:39.121198) updated (2025-02-03 13:32:39.149673) 2 out of 7 (2025-02-03 13:32:39.14993) updated (2025-02-03 13:32:39.161474) 3 out of 7 (2025-02-03 13:32:39.161706) updated (2025-02-03 13:32:39.173063) 4 out of 7 (2025-02-03 13:32:39.173269) updated (2025-02-03 13:32:39.188232) 5 out of 7 (2025-02-03 13:32:39.18845) updated (2025-02-03 13:32:39.210163) 6 out of 7 (2025-02-03 13:32:39.210419) updated (2025-02-03 13:32:39.222135) 7 out of 7 (2025-02-03 13:32:39.222346) updated (2025-02-03 13:32:39.233816) Next, identify the best-matching hexagon/rectangle for the input data (2025-02-03 13:32:39.234062)... Finally, append the response data (hits and mqe) into the sMap object (2025-02-03 13:32:39.245311)... 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: 2.08253616919154 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 2025-02-03 13:32:39.540519 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