############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data concordexR ### ############################################################################## ############################################################################## * checking for file ‘concordexR/DESCRIPTION’ ... OK * preparing ‘concordexR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘concordex-nonspatial.Rmd’ using rmarkdown --- finished re-building ‘concordex-nonspatial.Rmd’ --- re-building ‘overview.Rmd’ using rmarkdown Quitting from overview.Rmd:45-50 [example] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! failed to load resource name: EH7561 title: Small demo subset of mouse skeletal muscle Visium data reason: require("SpatialFeatureExperiment") failed: use BiocManager::install() to install package? --- Backtrace: ▆ 1. └─SFEData::McKellarMuscleData("small") 2. ├─ds[[id, force = force, verbose = verbose]] 3. └─ds[[id, force = force, verbose = verbose]] 4. └─ExperimentHub (local) .local(x, i, j = j, ...) 5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose) 6. │ └─base::eval(call, callEnv) 7. │ └─base::eval(call, callEnv) 8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose) 9. └─AnnotationHub (local) .local(x, i, j = j, ...) 10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 11. └─base::tryCatch(...) 12. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. └─value[[3L]](cond) 15. └─base::tryCatch(...) 16. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 17. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 18. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'overview.Rmd' failed with diagnostics: failed to load resource name: EH7561 title: Small demo subset of mouse skeletal muscle Visium data reason: require("SpatialFeatureExperiment") failed: use BiocManager::install() to install package? --- failed re-building ‘overview.Rmd’ SUMMARY: processing the following file failed: ‘overview.Rmd’ Error: Vignette re-building failed. Execution halted