Back to Build/check report for BioC 3.23 experimental data
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2026-01-13 15:01 -0500 (Tue, 13 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" 4848
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 235/432HostnameOS / ArchINSTALLBUILDCHECK
MerfishData 1.13.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2026-01-13 07:00 -0500 (Tue, 13 Jan 2026)
git_url: https://git.bioconductor.org/packages/MerfishData
git_branch: devel
git_last_commit: ef1e293
git_last_commit_date: 2025-10-29 10:05:03 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for MerfishData on nebbiolo1

To the developers/maintainers of the MerfishData package:
- 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: MerfishData
Version: 1.13.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MerfishData
StartedAt: 2026-01-13 11:30:51 -0500 (Tue, 13 Jan 2026)
EndedAt: 2026-01-13 11:38:53 -0500 (Tue, 13 Jan 2026)
EllapsedTime: 482.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MerfishData
###
##############################################################################
##############################################################################


* checking for file ‘MerfishData/DESCRIPTION’ ... OK
* preparing ‘MerfishData’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Merfish_mouse_colon_ibd.Rmd’ using rmarkdown
--- finished re-building ‘Merfish_mouse_colon_ibd.Rmd’

--- re-building ‘Merfish_mouse_hypothalamus.Rmd’ using rmarkdown
--- finished re-building ‘Merfish_mouse_hypothalamus.Rmd’

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

Quitting from Merfish_mouse_ileum.Rmd:223-230 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 26420 rows, data has 1
---
Backtrace:
    ▆
 1. └─scater::plotXY(sub.mol.dat, "gene", mem.img)
 2.   ├─base::`$<-`(`*tmp*`, "X", value = `<chr>`)
 3.   └─base::`$<-.data.frame`(`*tmp*`, "X", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Merfish_mouse_ileum.Rmd' failed with diagnostics:
replacement has 26420 rows, data has 1
--- failed re-building ‘Merfish_mouse_ileum.Rmd’

SUMMARY: processing the following file failed:
  ‘Merfish_mouse_ileum.Rmd’

Error: Vignette re-building failed.
Execution halted