############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r GEOmetadb -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GEOmetadb ### ############################################################################## ############################################################################## * checking for file 'GEOmetadb/DESCRIPTION' ... OK * preparing 'GEOmetadb': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'GEOmetadb.Rmd' using rmarkdown Loading required package: GEOquery Loading required package: Biobase Loading required package: BiocGenerics 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, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading required package: RSQLite trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz' Warning in download.file(url_geo, destfile = localfile, mode = "wb") : URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz': Timeout of 300 seconds was reached Quitting from lines 88-97 (GEOmetadb.Rmd) Error: processing vignette 'GEOmetadb.Rmd' failed with diagnostics: cannot open URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz' --- failed re-building 'GEOmetadb.Rmd' SUMMARY: processing the following file failed: 'GEOmetadb.Rmd' Error: Vignette re-building failed. Execution halted