| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-01-21 11:47 -0500 (Tue, 21 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4502 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4467 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4422 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4406 |
| 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 2082/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Hai Fang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
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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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: supraHex |
| Version: 1.45.1 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data supraHex |
| StartedAt: 2025-01-21 03:03:40 -0000 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 03:03:55 -0000 (Tue, 21 Jan 2025) |
| EllapsedTime: 15.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### 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 2025-01-21 03:03:52.734967 First, define topology of a map grid (2025-01-21 03:03:52.736107)... Second, initialise the codebook matrix (169 X 6) using 'linear' initialisation, given a topology and input data (2025-01-21 03:03:52.736107)... Third, get training at the rough stage (2025-01-21 03:03:52.757024)... 1 out of 2 (2025-01-21 03:03:52.759943) updated (2025-01-21 03:03:52.791323) 2 out of 2 (2025-01-21 03:03:52.791885) updated (2025-01-21 03:03:52.824225) Fourth, get training at the finetune stage (2025-01-21 03:03:52.824893)... 1 out of 7 (2025-01-21 03:03:52.826948) updated (2025-01-21 03:03:52.859648) 2 out of 7 (2025-01-21 03:03:52.860232) updated (2025-01-21 03:03:52.900129) 3 out of 7 (2025-01-21 03:03:52.900656) updated (2025-01-21 03:03:52.928153) 4 out of 7 (2025-01-21 03:03:52.928675) updated (2025-01-21 03:03:52.956559) 5 out of 7 (2025-01-21 03:03:52.957099) updated (2025-01-21 03:03:52.995269) 6 out of 7 (2025-01-21 03:03:52.995803) updated (2025-01-21 03:03:53.023268) 7 out of 7 (2025-01-21 03:03:53.023784) updated (2025-01-21 03:03:53.051585) Next, identify the best-matching hexagon/rectangle for the input data (2025-01-21 03:03:53.052148)... Finally, append the response data (hits and mqe) into the sMap object (2025-01-21 03:03:53.089522)... 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: 1.98434388468297 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 2025-01-21 03:03:53.730955 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