David Goldberg
| Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/knowYourCG |
| git_branch: devel |
| git_last_commit: a93c3a9 |
| git_last_commit_date: 2026-04-28 09:02:45 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 1134/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| knowYourCG 1.9.0 (landing page) David Goldberg
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | ||||||||||
| See other builds for knowYourCG in R Universe. | ||||||||||||||
|
To the developers/maintainers of the knowYourCG package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/knowYourCG.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: knowYourCG |
| Version: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data knowYourCG |
| StartedAt: 2026-05-18 18:29:49 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 18:31:33 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 104.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data knowYourCG
###
##############################################################################
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* checking for file ‘knowYourCG/DESCRIPTION’ ... OK
* preparing ‘knowYourCG’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Array.Rmd’ using rmarkdown
--- finished re-building ‘Array.Rmd’
--- re-building ‘Continuous.Rmd’ using rmarkdown
--- finished re-building ‘Continuous.Rmd’
--- re-building ‘Sequencing.Rmd’ using rmarkdown
trying URL 'https://zenodo.org/records/18175656/files/ChromHMM.20220414.cm'
Content type 'application/octet-stream' length 877986 bytes (857 KB)
==================================================
downloaded 857 KB
trying URL 'https://zenodo.org/records/18176004/files/mm10_f3_10cells.cg'
Content type 'application/octet-stream' length 11959677 bytes (11.4 MB)
==================================================
downloaded 11.4 MB
--- finished re-building ‘Sequencing.Rmd’
--- re-building ‘visualization.Rmd’ using rmarkdown
Quitting from visualization.Rmd:107-116 [ky21]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `stopAndCache()`:
!
| File HM450.address either not found or needs to be cached to be
| used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache("HM450.address")
| or download all data
| > sesameDataCache()
| to retrieve and cache needed sesame data.
---
Backtrace:
▆
1. └─knowYourCG::KYCG_plotManhattan(...)
2. └─sesameData::sesameData_getManifestGRanges(platform, genome = genome)
3. └─sesameData::sesameDataGet(sprintf("%s.address", platform))
4. ├─base::suppressMessages(log <- capture.output(obj <- .sesameDataGet(title)))
5. │ └─base::withCallingHandlers(...)
6. ├─utils::capture.output(obj <- .sesameDataGet(title))
7. │ └─base::withVisible(...elt(i))
8. └─sesameData:::.sesameDataGet(title)
9. └─sesameData:::stopAndCache(title)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
| File HM450.address either not found or needs to be cached to be
| used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache("HM450.address")
| or download all data
| > sesameDataCache()
| to retrieve and cache needed sesame data.
--- failed re-building ‘visualization.Rmd’
SUMMARY: processing the following file failed:
‘visualization.Rmd’
Error: Vignette re-building failed.
Execution halted