############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data XeniumIO ### ############################################################################## ############################################################################## * checking for file ‘XeniumIO/DESCRIPTION’ ... OK * preparing ‘XeniumIO’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘XeniumIO.Rmd’ using rmarkdown Quitting from XeniumIO.Rmd:181-187 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! NotImplemented: Support for codec 'zstd' not built In order to read this file, you will need to reinstall arrow with additional features enabled. Set one of these environment variables before installing: * Sys.setenv(LIBARROW_MINIMAL = "false") (for all optional features, including 'zstd') * Sys.setenv(ARROW_WITH_ZSTD = "ON") (for just 'zstd') See https://arrow.apache.org/docs/r/articles/install.html for details --- Backtrace: ▆ 1. ├─BiocIO::import(TENxXenium(xeniumOut = outfold), ref = "Gene Expression") 2. └─XeniumIO::import(TENxXenium(xeniumOut = outfold), ref = "Gene Expression") 3. ├─BiocIO::import(con@colData) 4. └─VisiumIO::import(con@colData) 5. └─arrow::read_parquet(path(con)) 6. └─base::tryCatch(reader$ReadTable(), error = read_compressed_error) 7. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'XeniumIO.Rmd' failed with diagnostics: NotImplemented: Support for codec 'zstd' not built In order to read this file, you will need to reinstall arrow with additional features enabled. Set one of these environment variables before installing: * Sys.setenv(LIBARROW_MINIMAL = "false") (for all optional features, including 'zstd') * Sys.setenv(ARROW_WITH_ZSTD = "ON") (for just 'zstd') See https://arrow.apache.org/docs/r/articles/install.html for details --- failed re-building ‘XeniumIO.Rmd’ SUMMARY: processing the following file failed: ‘XeniumIO.Rmd’ Error: Vignette re-building failed. Execution halted