Error(s) in re-building vignettes:
  ...
--- re-building 'metaboGSE.Rmd' using rmarkdown
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ape
Loading required package: glpkAPI
using GLPK version 4.65

Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:Matrix':

    which

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, which.max, which.min

Loading required package: graph

Attaching package: 'graph'

The following objects are masked from 'package:ape':

    complement, edges

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:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid

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

The following objects are masked from 'package:sybil':

    algorithm, algorithm<-, allGenes, genes


Building most specific GOs .....
	( 2324 GO terms found. )

Build GO DAG topology ..........
	( 4598 GO terms and 10232 relations. )

Annotating nodes ...............
	( 3620 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 963 nontrivial nodes
		 parameters: 
			 test statistic: fisher

	 Level 16:	1 nodes to be scored	(0 eliminated genes)

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

	 Level 14:	4 nodes to be scored	(8 eliminated genes)

	 Level 13:	11 nodes to be scored	(8 eliminated genes)

	 Level 12:	17 nodes to be scored	(22 eliminated genes)

	 Level 11:	33 nodes to be scored	(207 eliminated genes)

	 Level 10:	85 nodes to be scored	(446 eliminated genes)

	 Level 9:	106 nodes to be scored	(861 eliminated genes)

	 Level 8:	113 nodes to be scored	(1243 eliminated genes)

	 Level 7:	135 nodes to be scored	(1599 eliminated genes)

	 Level 6:	170 nodes to be scored	(2293 eliminated genes)

	 Level 5:	150 nodes to be scored	(2941 eliminated genes)

	 Level 4:	83 nodes to be scored	(3177 eliminated genes)

	 Level 3:	42 nodes to be scored	(3432 eliminated genes)

	 Level 2:	11 nodes to be scored	(3531 eliminated genes)

	 Level 1:	1 nodes to be scored	(3575 eliminated genes)
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building 'metaboGSE.Rmd'

SUMMARY: processing the following file failed:
  'metaboGSE.Rmd'

Error: Vignette re-building failed.
Execution halted