| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-23 12:09 -0400 (Mon, 23 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4565 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4544 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4492 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4496 |
| 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 1235/2310 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methrix 1.23.0 (landing page) Anand Mayakonda
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | 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 | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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To the developers/maintainers of the methrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methrix.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: methrix |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 methrix |
| StartedAt: 2025-06-22 17:49:23 -0400 (Sun, 22 Jun 2025) |
| EndedAt: 2025-06-22 17:50:17 -0400 (Sun, 22 Jun 2025) |
| EllapsedTime: 54.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 methrix
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* checking for file ‘methrix/DESCRIPTION’ ... OK
* preparing ‘methrix’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘methrix.Rmd’ using rmarkdown
Quitting from methrix.Rmd:107-110 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `standardChromosomes()`:
! could not find function "standardChromosomes"
---
Backtrace:
▆
1. ├─base::suppressWarnings(methrix::extract_CPGs(ref_genome = "BSgenome.Hsapiens.UCSC.hg19"))
2. │ └─base::withCallingHandlers(...)
3. └─methrix::extract_CPGs(ref_genome = "BSgenome.Hsapiens.UCSC.hg19")
4. └─data.table::data.table(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'methrix.Rmd' failed with diagnostics:
could not find function "standardChromosomes"
--- failed re-building ‘methrix.Rmd’
SUMMARY: processing the following file failed:
‘methrix.Rmd’
Error: Vignette re-building failed.
Execution halted