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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PloGO2
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* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* preparing ‘PloGO2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘PloGO2_vignette.Rnw’ using Sweave
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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, aperm, 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: 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: IRanges
Loading required package: S4Vectors
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: GOstats
Loading required package: Category
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Loading required package: graph
Attaching package: ‘GOstats’
The following object is masked from ‘package:AnnotationDbi’:
makeGOGraph
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [rest.uniprot.org] SSL connection timeout
Error in getUniprotBatch(values = Uniprot[from[jj]:to[jj]], attributes = c("accession", :
Error downloading records from Uniprot
Error: processing vignette 'PloGO2_vignette.Rnw' failed with diagnostics:
chunk 2 (label = genFile)
Error in bm.res[, 2] : incorrect number of dimensions
--- failed re-building ‘PloGO2_vignette.Rnw’
--- re-building ‘PloGO2_with_WGNCA_vignette.Rnw’ using Sweave
Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Attaching package: ‘WGCNA’
The following object is masked from ‘package:IRanges’:
cor
The following object is masked from ‘package:S4Vectors’:
cor
The following object is masked from ‘package:stats’:
cor
dev.new(): using pdf(file="Rplots1.pdf")
--- finished re-building ‘PloGO2_with_WGNCA_vignette.Rnw’
SUMMARY: processing the following file failed:
‘PloGO2_vignette.Rnw’
Error: Vignette re-building failed.
Execution halted
