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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4013
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Package 311/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellxgenedp 1.15.0  (landing page)
Martin Morgan
Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025)
git_url: https://git.bioconductor.org/packages/cellxgenedp
git_branch: devel
git_last_commit: 844e4cf
git_last_commit_date: 2025-10-29 11:15:13 -0500 (Wed, 29 Oct 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for cellxgenedp on kjohnson3

To the developers/maintainers of the cellxgenedp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellxgenedp.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: cellxgenedp
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cellxgenedp
StartedAt: 2025-11-12 15:57:10 -0500 (Wed, 12 Nov 2025)
EndedAt: 2025-11-12 15:57:46 -0500 (Wed, 12 Nov 2025)
EllapsedTime: 36.4 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 cellxgenedp
###
##############################################################################
##############################################################################


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

Quitting from a_using_cellxgenedp.Rmd:330-333 [readH5AD]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'rhdf5'
---
Backtrace:
    ▆
 1. ├─zellkonverter::readH5AD(local_file, use_hdf5 = TRUE, reader = "R")
 2. │ └─zellkonverter:::.native_reader(file, backed = use_hdf5, verbose = verbose)
 3. │   └─zellkonverter:::.list_contents(file)
 4. └─base::loadNamespace(x)
 5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 6.     └─base (local) withOneRestart(expr, restarts[[1L]])
 7.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'a_using_cellxgenedp.Rmd' failed with diagnostics:
there is no package called 'rhdf5'
--- failed re-building ‘a_using_cellxgenedp.Rmd’

--- re-building ‘b_case_studies.Rmd’ using rmarkdown
[WARNING] Duplicate link reference '[OLSr]' at b_case_studies.knit.md line 580 column 1
--- finished re-building ‘b_case_studies.Rmd’

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

Error: Vignette re-building failed.
Execution halted