############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data LRBaseDbi ### ############################################################################## ############################################################################## * checking for file ‘LRBaseDbi/DESCRIPTION’ ... OK * preparing ‘LRBaseDbi’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘LRBaseDbi.Rnw’ using Sweave LRBase.XXX.eg.db-type packages are deprecated since Bioconductor 3.14. Use AnnotationHub instead. For details, check the vignette of LRBaseDbi Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: BiocFileCache Loading required package: dbplyr Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead Error while performing HEAD request. Proceeding without cache information. Warning: download failed web resource path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’ local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/AnnotationHub/file15e056edd12d9’ reason: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_disk()`: ! Timeout was reached [annotationhub.bioconductor.org]: Connection timed out after 10003 milliseconds Warning: bfcdownload() failed rid: BFC1 file: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’ reason: download failed Warning: Could not check database for updates. Database source currently unreachable. This should only be a temporary interruption. Using previously cached version. Error: processing vignette 'LRBaseDbi.Rnw' failed with diagnostics: chunk 2 Error in value[[3L]](cond) : 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 10003 milliseconds Consider rerunning with 'localHub=TRUE' --- failed re-building ‘LRBaseDbi.Rnw’ SUMMARY: processing the following file failed: ‘LRBaseDbi.Rnw’ Error: Vignette re-building failed. Execution halted