| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-03 11:33 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4775 |
| 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 2048/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.13.0 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
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. |
| 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: 2025-11-02 20:06:17 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 20:08:11 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 114.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialFeatureExperiment
###
##############################################################################
##############################################################################
* 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