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This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 1493/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 2.20.1  (landing page)
Mike Jiang
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/openCyto
git_branch: RELEASE_3_21
git_last_commit: 5269a79
git_last_commit_date: 2025-08-25 20:07:28 -0400 (Mon, 25 Aug 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

BUILD results for openCyto on kjohnson1

To the developers/maintainers of the openCyto package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openCyto.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: openCyto
Version: 2.20.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data openCyto
StartedAt: 2025-09-23 05:55:17 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 05:56:02 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 45.4 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 openCyto
###
##############################################################################
##############################################################################


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

Quitting from HowToAutoGating.Rmd:43-49 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `add_ggcyto()`:
! object '+.gg' not found
---
Backtrace:
     ▆
  1. ├─ggplot2::autoplot(fr, chnl)
  2. └─ggcyto:::autoplot.flowFrame(fr, chnl)
  3.   ├─ggplot2::autoplot(object, x = x, ...)
  4.   └─ggcyto:::autoplot.flowSet(object, x = x, ...)
  5.     ├─ggcyto::ggcyto(object, aes_q(x = as.symbol(x)), ...)
  6.     └─ggcyto:::ggcyto.flowSet(object, aes_q(x = as.symbol(x)), ...)
  7.       ├─p + ggcyto_par_default()
  8.       └─p + ggcyto_par_default()
  9.         └─ggcyto:::add_ggcyto(e1, e2, e2name)
 10.           ├─e1 + e2.new
 11.           └─e1 + e2.new
 12.             └─ggcyto:::add_ggcyto(e1, e2, e2name)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

--- re-building ‘openCytoVignette.Rmd’ using knitr
2025-09-23 05:56:01.018 R[97991:396837305] XType: Using static font registry.

Quitting from openCytoVignette.Rmd:68-71 [plot-manual-gates]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `add_ggcyto()`:
! object '+.gg' not found
---
Backtrace:
     ▆
  1. ├─ggplot2::autoplot(gh)
  2. └─ggcyto:::autoplot.GatingHierarchy(gh)
  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 'openCytoVignette.Rmd' failed with diagnostics:
object '+.gg' not found
--- failed re-building ‘openCytoVignette.Rmd’

SUMMARY: processing the following files failed:
  ‘HowToAutoGating.Rmd’ ‘openCytoVignette.Rmd’

Error: Vignette re-building failed.
Execution halted