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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data topGO
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* checking for file ‘topGO/DESCRIPTION’ ... OK
* preparing ‘topGO’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘topGO.Rnw’ using Sweave

Loading required package: xtable
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

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 object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: SparseM

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: ‘topGO’

The following object is masked from ‘package:IRanges’:

    members

Loading required package: org.Hs.eg.db



Building most specific GOs .....
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
	( 1676 GO terms found. )

Build GO DAG topology ..........
	( 4296 GO terms and 9327 relations. )

Annotating nodes ...............
	( 316 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 857 nontrivial nodes
		 parameters: 
			 test statistic: fisher

			 -- Classic Algorithm -- 

		 the algorithm is scoring 943 nontrivial nodes
		 parameters: 
			 test statistic: ks
			 score order: increasing

			 -- Elim Algorithm -- 

		 the algorithm is scoring 943 nontrivial nodes
		 parameters: 
			 test statistic: ks
			 cutOff: 0.01
			 score order: increasing

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	1 nodes to be scored	(0 eliminated genes)

	 Level 13:	4 nodes to be scored	(0 eliminated genes)

	 Level 12:	15 nodes to be scored	(25 eliminated genes)

	 Level 11:	37 nodes to be scored	(35 eliminated genes)

	 Level 10:	69 nodes to be scored	(55 eliminated genes)

	 Level 9:	96 nodes to be scored	(74 eliminated genes)

	 Level 8:	116 nodes to be scored	(148 eliminated genes)

	 Level 7:	143 nodes to be scored	(159 eliminated genes)

	 Level 6:	158 nodes to be scored	(178 eliminated genes)

	 Level 5:	143 nodes to be scored	(184 eliminated genes)

	 Level 4:	95 nodes to be scored	(208 eliminated genes)

	 Level 3:	50 nodes to be scored	(228 eliminated genes)

	 Level 2:	14 nodes to be scored	(236 eliminated genes)

	 Level 1:	1 nodes to be scored	(236 eliminated genes)
Loading required package: Rgraphviz
Loading required package: grid

Attaching package: ‘grid’

The following object is masked from ‘package:topGO’:

    depth


Attaching package: ‘Rgraphviz’

The following objects are masked from ‘package:IRanges’:

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to


Building most specific GOs .....
	( 109 GO terms found. )

Build GO DAG topology ..........
	( 223 GO terms and 286 relations. )

Annotating nodes ...............
	( 86 genes annotated to the GO terms. )
Loading required package: multtest

Building most specific GOs .....
	( 7546 GO terms found. )

Build GO DAG topology ..........
	( 11105 GO terms and 24472 relations. )

Annotating nodes ...............
	( 3879 genes annotated to the GO terms. )
Warning in .genesInNode(graph(object), whichGO) :
  Nodes not present in the graph:GO:0044255

Error: processing vignette 'topGO.Rnw' failed with diagnostics:
 chunk 48 
Error in genesInTerm(GOdata, goID)[[1]] : subscript out of bounds

--- failed re-building ‘topGO.Rnw’

SUMMARY: processing the following file failed:
  ‘topGO.Rnw’

Error: Vignette re-building failed.
Execution halted