############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/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 to build vignettes * creating vignettes ... ERROR --- re-building ‘SFE.Rmd’ using rmarkdown /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' Quitting from SFE.Rmd:440-443 [unnamed-chunk-62] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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