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This page was generated on 2025-11-01 11:33 -0400 (Sat, 01 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4774
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 2048/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialFeatureExperiment 1.13.0  (landing page)
Lambda Moses
Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025)
git_url: https://git.bioconductor.org/packages/SpatialFeatureExperiment
git_branch: devel
git_last_commit: 06f0dbf
git_last_commit_date: 2025-10-29 11:19:11 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for SpatialFeatureExperiment on nebbiolo1

To the developers/maintainers of the SpatialFeatureExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialFeatureExperiment.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: SpatialFeatureExperiment
Version: 1.13.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialFeatureExperiment
StartedAt: 2025-10-31 20:21:15 -0400 (Fri, 31 Oct 2025)
EndedAt: 2025-10-31 20:23:08 -0400 (Fri, 31 Oct 2025)
EllapsedTime: 113.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialFeatureExperiment
###
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* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* preparing ‘SpatialFeatureExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SFE.Rmd’ using rmarkdown
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'

Quitting from SFE.Rmd:440-443 [unnamed-chunk-62]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'con' in selecting a method for function 'import': The 'spatial' directory was not found.
---
Backtrace:
    ▆
 1. ├─BiocIO::import(...)
 2. ├─VisiumIO::TENxVisium(...)
 3. │ └─VisiumIO:::.find_convert_resources(...)
 4. │   ├─base::dirname(...)
 5. │   └─VisiumIO:::.getSpatialPath(...)
 6. │     └─base::stop("The 'spatial' directory was not found.")
 7. └─base::.handleSimpleError(...)
 8.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SFE.Rmd' failed with diagnostics:
error in evaluating the argument 'con' in selecting a method for function 'import': The 'spatial' directory was not found.
--- failed re-building ‘SFE.Rmd’

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

Error: Vignette re-building failed.
Execution halted