############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GRaNIE ### ############################################################################## ############################################################################## * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * preparing ‘GRaNIE’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘GRaNIE_workflow.Rmd’ using rmarkdown ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.5 ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.4.1 ✔ readr 2.1.3 ✔ forcats 0.5.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Loading required package: topGO Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union 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 Attaching package: 'graph' The following object is masked from 'package:stringr': boundary 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:dplyr': first, rename The following object is masked from 'package:tidyr': expand The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice The following object is masked from 'package:purrr': reduce Attaching package: 'AnnotationDbi' The following object is masked from 'package:dplyr': select 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 Welcome to the GRaNIE package and thank you for using our software. This is GRaNIE version 1.0.7. All project-related information, guidance, help, documentation and ways to contact us can be found in the R help or here: https://grp-zaugg.embl-community.io/GRaNIE Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand The following objects are masked from 'package:tidyr': expand, pack, unpack Ensembl site unresponsive, trying asia mirror Quitting from lines 356-359 (GRaNIE_workflow.Rmd) Error: processing vignette 'GRaNIE_workflow.Rmd' failed with diagnostics: Gateway Timeout (HTTP 504). --- failed re-building ‘GRaNIE_workflow.Rmd’ SUMMARY: processing the following file failed: ‘GRaNIE_workflow.Rmd’ Error: Vignette re-building failed. Execution halted