Multiple platform build/check report for BioC 3.23 - BUILD results for knowYourCG on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4826
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4561
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4562
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*

BUILD results for knowYourCG on lconway

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.

raw results

Summary

Package: knowYourCG

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data knowYourCG

StartedAt: 2025-11-17 17:41:46 -0500 (Mon, 17 Nov 2025)

EndedAt: 2025-11-17 17:42:39 -0500 (Mon, 17 Nov 2025)

EllapsedTime: 52.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data knowYourCG
###
##############################################################################
##############################################################################


* 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

Quitting from Array.Rmd:38-50 [ky1, load-depenencies]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 1 resources failed to download
---
Backtrace:
    ▆
 1. └─sesameData::sesameDataCache(...)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Array.Rmd' failed with diagnostics:
1 resources failed to download
--- failed re-building ‘Array.Rmd’

--- re-building ‘Continuous.Rmd’ using rmarkdown

Quitting from Continuous.Rmd:42-45 [ky21, run-test-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `stopAndCache()`:
! 
| File KYCG.MM285.designGroup.20210210 either not found or needs to be cached to be
| used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache("KYCG.MM285.designGroup.20210210")
| or download all data
| > sesameDataCache()
| to retrieve and cache needed sesame data.
---
Backtrace:
     ▆
  1. └─knowYourCG::getDBs("KYCG.MM285.designGroup")
  2.   ├─base::do.call(...)
  3.   └─base::lapply(...)
  4.     └─knowYourCG (local) FUN(X[[i]], ...)
  5.       └─sesameData::sesameDataGet(nm)
  6.         ├─base::suppressMessages(log <- capture.output(obj <- .sesameDataGet(title)))
  7.         │ └─base::withCallingHandlers(...)
  8.         ├─utils::capture.output(obj <- .sesameDataGet(title))
  9.         │ └─base::withVisible(...elt(i))
 10.         └─sesameData:::.sesameDataGet(title)
 11.           └─sesameData:::stopAndCache(title)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Continuous.Rmd' failed with diagnostics:

| File KYCG.MM285.designGroup.20210210 either not found or needs to be cached to be
| used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache("KYCG.MM285.designGroup.20210210")
| or download all data
| > sesameDataCache()
| to retrieve and cache needed sesame data.
--- failed re-building ‘Continuous.Rmd’

--- re-building ‘Sequencing.Rmd’ using rmarkdown
trying URL 'https://github.com/zhou-lab/KYCGKB_mm10/raw/refs/heads/main/ChromHMM.20220414.cm'
Content type 'application/octet-stream' length 877986 bytes (857 KB)
==================================================
downloaded 857 KB

trying URL 'https://github.com/zhou-lab/YAME/raw/refs/heads/main/test/input/single_cell_10_samples.cg'
Content type 'application/octet-stream' length 11610328 bytes (11.1 MB)
==================================================
downloaded 11.1 MB

2025-11-17 17:42:33.153 R[81215:16359440] XType: Using static font registry.
--- finished re-building ‘Sequencing.Rmd’

SUMMARY: processing the following files failed:
  ‘Array.Rmd’ ‘Continuous.Rmd’

Error: Vignette re-building failed.
Execution halted