############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data visiumStitched ### ############################################################################## ############################################################################## * checking for file ‘visiumStitched/DESCRIPTION’ ... OK * preparing ‘visiumStitched’: * checking DESCRIPTION meta-information ... OK * installing the package (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘misc.Rmd’ using rmarkdown 2025-12-12 18:09:40.229 R[13618:378683341] XType: Using static font registry. --- finished re-building ‘misc.Rmd’ --- re-building ‘visiumStitched.Rmd’ using rmarkdown Quitting from visiumStitched.Rmd:472-489 [precast_k2_stitched] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `value[[3L]]()`: ! failed to connect reason: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached [bioconductor.org]: Connection timed out after 10004 milliseconds Consider rerunning with 'localHub=TRUE' --- Backtrace: ▆ 1. └─spatialLIBD::fetch_data(type = "visiumStitched_brain_spe") 2. ├─base::stopifnot(methods::is(eh, "ExperimentHub")) 3. ├─methods::is(eh, "ExperimentHub") 4. └─ExperimentHub::ExperimentHub() 5. └─AnnotationHub::.Hub(...) 6. └─base::tryCatch(...) 7. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'visiumStitched.Rmd' failed with diagnostics: failed to connect reason: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached [bioconductor.org]: Connection timed out after 10004 milliseconds Consider rerunning with 'localHub=TRUE' --- failed re-building ‘visiumStitched.Rmd’ SUMMARY: processing the following file failed: ‘visiumStitched.Rmd’ Error: Vignette re-building failed. Execution halted