############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/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 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")'. 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 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 c(from, to) : closing unused connection 7 (<-localhost:11339) Warning in c(from, to) : closing unused connection 6 (<-localhost:11339) converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates Ensembl site unresponsive, trying uswest mirror Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics: chunk 34 (label = main_gsea) Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: unable to get local issuer certificate --- failed re-building ‘SeqGSEA.Rnw’ SUMMARY: processing the following file failed: ‘SeqGSEA.Rnw’ Error: Vignette re-building failed. Execution halted