############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BgeeDB ### ############################################################################## ############################################################################## * checking for file ‘BgeeDB/DESCRIPTION’ ... OK * preparing ‘BgeeDB’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘BgeeDB_Manual.Rmd’ using rmarkdown Loading required package: topGO 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 Loading required package: graph Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: SparseM Attaching package: 'SparseM' The following object is masked from 'package:base': backsolve groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:S4Vectors': expand Quitting from lines 85-93 (BgeeDB_Manual.Rmd) Error: processing vignette 'BgeeDB_Manual.Rmd' failed with diagnostics: cannot open URL 'ftp://ftp.bgee.org/bgee_v15_0/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM.tar.gz' --- failed re-building ‘BgeeDB_Manual.Rmd’ SUMMARY: processing the following file failed: ‘BgeeDB_Manual.Rmd’ Error: Vignette re-building failed. Execution halted