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This page was generated on 2025-09-13 12:04 -0400 (Sat, 13 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 504/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.21.0  (landing page)
Mike Jiang
Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 Sep 2025)
git_url: https://git.bioconductor.org/packages/CytoML
git_branch: devel
git_last_commit: 14d4f19
git_last_commit_date: 2025-04-15 11:03:15 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for CytoML on lconway

To the developers/maintainers of the CytoML package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoML.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: CytoML
Version: 2.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CytoML
StartedAt: 2025-09-12 16:29:55 -0400 (Fri, 12 Sep 2025)
EndedAt: 2025-09-12 16:31:28 -0400 (Fri, 12 Sep 2025)
EllapsedTime: 93.7 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 CytoML
###
##############################################################################
##############################################################################


* checking for file ‘CytoML/DESCRIPTION’ ... OK
* preparing ‘CytoML’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HowToExportGatingSet.Rmd’ using rmarkdown

Quitting from HowToExportGatingSet.Rmd:52-71 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `add_ggcyto()`:
! object '+.gg' not found
---
Backtrace:
     ▆
  1. ├─ggplot2::autoplot(gs[[1]])
  2. └─ggcyto:::autoplot.GatingHierarchy(gs[[1]])
  3.   ├─BiocGenerics::lapply(...)
  4.   └─base::lapply(...)
  5.     └─ggcyto (local) FUN(X[[i]], ...)
  6.       └─ggcyto:::autoplot.GatingSet(object, gate, y = y, ...)
  7.         ├─ggcyto::ggcyto(object, mapping, ...)
  8.         └─ggcyto:::ggcyto.GatingHierarchy(object, mapping, ...)
  9.           ├─ggcyto::ggcyto(data, ...)
 10.           └─ggcyto:::ggcyto.GatingSet(data, ...)
 11.             └─ggcyto:::ggcyto.flowSet(data = data, mapping = mapping, ...)
 12.               ├─p + ggcyto_par_default()
 13.               └─p + ggcyto_par_default()
 14.                 └─ggcyto:::add_ggcyto(e1, e2, e2name)
 15.                   ├─e1 + e2.new
 16.                   └─e1 + e2.new
 17.                     └─ggcyto:::add_ggcyto(e1, e2, e2name)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'HowToExportGatingSet.Rmd' failed with diagnostics:
object '+.gg' not found
--- failed re-building ‘HowToExportGatingSet.Rmd’

--- re-building ‘cytobank2GatingSet.Rmd’ using rmarkdown

Quitting from cytobank2GatingSet.Rmd:58-64 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `add_ggcyto()`:
! object '+.gg' not found
---
Backtrace:
     ▆
  1. ├─ggplot2::autoplot(gs[[1]])
  2. └─ggcyto:::autoplot.GatingHierarchy(gs[[1]])
  3.   ├─BiocGenerics::lapply(...)
  4.   └─base::lapply(...)
  5.     └─ggcyto (local) FUN(X[[i]], ...)
  6.       └─ggcyto:::autoplot.GatingSet(object, gate, y = y, ...)
  7.         ├─ggcyto::ggcyto(object, mapping, ...)
  8.         └─ggcyto:::ggcyto.GatingHierarchy(object, mapping, ...)
  9.           ├─ggcyto::ggcyto(data, ...)
 10.           └─ggcyto:::ggcyto.GatingSet(data, ...)
 11.             └─ggcyto:::ggcyto.flowSet(data = data, mapping = mapping, ...)
 12.               ├─p + ggcyto_par_default()
 13.               └─p + ggcyto_par_default()
 14.                 └─ggcyto:::add_ggcyto(e1, e2, e2name)
 15.                   ├─e1 + e2.new
 16.                   └─e1 + e2.new
 17.                     └─ggcyto:::add_ggcyto(e1, e2, e2name)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cytobank2GatingSet.Rmd' failed with diagnostics:
object '+.gg' not found
--- failed re-building ‘cytobank2GatingSet.Rmd’

--- re-building ‘flowjo_to_gatingset.Rmd’ using rmarkdown
2025-09-12 16:31:21.492 R[50889:269243382] XType: com.apple.fonts is not accessible.
2025-09-12 16:31:21.492 R[50889:269243382] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘flowjo_to_gatingset.Rmd’

SUMMARY: processing the following files failed:
  ‘HowToExportGatingSet.Rmd’ ‘cytobank2GatingSet.Rmd’

Error: Vignette re-building failed.
Execution halted