##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data clipper
###
##############################################################################
##############################################################################


* checking for file ‘clipper/DESCRIPTION’ ... OK
* preparing ‘clipper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘clipper.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, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view
    with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

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: org.Hs.eg.db

Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Warning: replacing previous import ‘RBGL::maxClique’ by ‘gRbase::maxClique’ when loading ‘clipper’
Warning: replacing previous import ‘graph::addEdge’ by ‘gRbase::addEdge’ when loading ‘clipper’
Warning: replacing previous import ‘KEGGgraph::subGraph’ by ‘gRbase::subGraph’ when loading ‘clipper’
Warning: replacing previous import ‘KEGGgraph::nodes’ by ‘gRbase::nodes’ when loading ‘clipper’
Warning: replacing previous import ‘graph::connComp’ by ‘gRbase::connComp’ when loading ‘clipper’
Warning: replacing previous import ‘KEGGgraph::edges’ by ‘gRbase::edges’ when loading ‘clipper’
Warning: replacing previous import ‘graph::adj’ by ‘gRbase::adj’ when loading ‘clipper’
Warning: replacing previous import ‘graph::removeEdge’ by ‘gRbase::removeEdge’ when loading ‘clipper’

Error: processing vignette 'clipper.Rnw' failed with diagnostics:
 chunk 12 (label = pathQUsage) 
Error in stopifnot_igraph(object) : Not a graph object

--- failed re-building ‘clipper.Rnw’

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

Error: Vignette re-building failed.
Execution halted