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

--- re-building ‘graphite.Rnw’ using Sweave
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

Warning: Local storage of pathway data using format v1 was deprecated in graphite
1.55.1.
✔ graphite will automatically migrate to and use format v2 going forward.
ℹ If you no longer need compatibility with older graphite versions, run
  purgeCacheV1() to reclaim disk space.

Loading required package: KEGGgraph

Attaching package: ‘KEGGgraph’

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

    plot

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

    plot

Loading required package: AnnotationDbi
Loading required package: stats4
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: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns
No methods found in package ‘GenomeInfoDb’ for requests: ‘seqnames’, ‘seqlengths’, ‘seqlevels’ when loading ‘qpgraph’

Error: processing vignette 'graphite.Rnw' failed with diagnostics:
 chunk 17 (label = tg1) 
Error : package or namespace load failed for ‘topologyGSA’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'

--- failed re-building ‘graphite.Rnw’

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

Error: Vignette re-building failed.
Execution halted