############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SeqGSEA ### ############################################################################## ############################################################################## * checking for file ‘SeqGSEA/DESCRIPTION’ ... OK * preparing ‘SeqGSEA’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘SeqGSEA.Rnw’ using Sweave Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: doParallel Loading required package: foreach Loading required package: iterators Loading required package: parallel Loading required package: DESeq2 Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following objects are masked from ‘package:Biobase’: anyMissing, rowMedians Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars The following object is masked from ‘package:Biobase’: rowMedians Warning: executing %dopar% sequentially: no parallel backend registered converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates found already estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates Warning in for (i in seq_len(n)) { : closing unused connection 7 (<-localhost:11006) Warning in for (i in seq_len(n)) { : closing unused connection 6 (<-localhost:11006) converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics: chunk 34 (label = main_gsea) Error : Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable. Look at ?useEnsembl for details on how to try a mirror site. --- failed re-building ‘SeqGSEA.Rnw’ SUMMARY: processing the following file failed: ‘SeqGSEA.Rnw’ Error: Vignette re-building failed. Execution halted