############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data updateObject ### ############################################################################## ############################################################################## * checking for file ‘updateObject/DESCRIPTION’ ... OK * preparing ‘updateObject’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘updateObject.Rmd’ using rmarkdown Quitting from updateObject.Rmd:136-139 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! class "Seqinfo" is not exported by 'namespace:GenomeInfoDb' --- Backtrace: ▆ 1. └─updateObject::updateBiocPackageRepoObjects(...) 2. └─updateObject::updatePackageObjects(...) 3. └─updateObject::updateSerializedObjects(...) 4. └─updateObject::update_rda_file(filepath, filter = filter, dry.run = dry.run) 5. └─BiocGenerics:::attach_classdef_and_updateobjdef_pkgs(class(x)) 6. └─BiocGenerics:::.attach_namespace(classdef_pkg) 7. ├─base::suppressMessages(suppressWarnings(suppressPackageStartupMessages(attachNamespace(pkg)))) 8. │ └─base::withCallingHandlers(...) 9. ├─base::suppressWarnings(suppressPackageStartupMessages(attachNamespace(pkg))) 10. │ └─base::withCallingHandlers(...) 11. ├─base::suppressPackageStartupMessages(attachNamespace(pkg)) 12. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) 13. └─base::attachNamespace(pkg) 14. └─base::asNamespace(ns, base.OK = FALSE) 15. └─base::getNamespace(ns) 16. ├─.Internal(getRegisteredNamespace(name)) %||% ... 17. └─base::loadNamespace(name) 18. ├─base::namespaceImportFrom(...) 19. │ └─base::asNamespace(ns) 20. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 21. ├─base::namespaceImportFrom(...) 22. │ └─base::asNamespace(ns) 23. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 24. └─base::namespaceImportClasses(...) 25. └─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from) 26. └─base::importIntoEnv(impenv, impnames, ns, impvars) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'updateObject.Rmd' failed with diagnostics: class "Seqinfo" is not exported by 'namespace:GenomeInfoDb' --- failed re-building ‘updateObject.Rmd’ SUMMARY: processing the following file failed: ‘updateObject.Rmd’ Error: Vignette re-building failed. Execution halted