| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2130/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Hai Fang
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the supraHex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/supraHex.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: supraHex |
| Version: 1.46.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data supraHex |
| StartedAt: 2025-08-31 19:34:04 -0400 (Sun, 31 Aug 2025) |
| EndedAt: 2025-08-31 19:34:15 -0400 (Sun, 31 Aug 2025) |
| EllapsedTime: 11.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/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 2025-08-31 19:34:13.20075 First, define topology of a map grid (2025-08-31 19:34:13.201602)... Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-08-31 19:34:13.201602)... Third, get training at the rough stage (2025-08-31 19:34:13.216128)... 1 out of 2 (2025-08-31 19:34:13.218332) updated (2025-08-31 19:34:13.24233) 2 out of 2 (2025-08-31 19:34:13.242776) updated (2025-08-31 19:34:13.26644) Fourth, get training at the finetune stage (2025-08-31 19:34:13.2669)... 1 out of 7 (2025-08-31 19:34:13.26824) updated (2025-08-31 19:34:13.293079) 2 out of 7 (2025-08-31 19:34:13.293458) updated (2025-08-31 19:34:13.310609) 3 out of 7 (2025-08-31 19:34:13.311001) updated (2025-08-31 19:34:13.331228) 4 out of 7 (2025-08-31 19:34:13.331611) updated (2025-08-31 19:34:13.352177) 5 out of 7 (2025-08-31 19:34:13.352576) updated (2025-08-31 19:34:13.375837) 6 out of 7 (2025-08-31 19:34:13.376219) updated (2025-08-31 19:34:13.393225) 7 out of 7 (2025-08-31 19:34:13.393593) updated (2025-08-31 19:34:13.410536) Next, identify the best-matching hexagon/rectangle for the input data (2025-08-31 19:34:13.410939)... Finally, append the response data (hits and mqe) into the sMap object (2025-08-31 19:34:13.426275)... 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: 2.02512980511463 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 2025-08-31 19:34:13.826271 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