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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data KEGGgraph
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* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* preparing ‘KEGGgraph’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘KEGGgraph.Rnw’ using Sweave
Attaching package: ‘KEGGgraph’
The following object is masked from ‘package:graphics’:
plot
The following object is masked from ‘package:base’:
plot
Loading required package: graph
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: grid
Loading required package: org.Hs.eg.db
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 objects are masked from ‘package:Rgraphviz’:
from, to
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Warning in arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor, :
zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor, :
zero-length arrow is of indeterminate angle and so skipped
Error: processing vignette 'KEGGgraph.Rnw' failed with diagnostics:
chunk 20 (label = cnexample)
Error in buildEdgeList(graph, recipEdges, edgeAttrs, subGList, attrs$edge) :
attempt to set index 64/64 in SET_STRING_ELT
--- failed re-building ‘KEGGgraph.Rnw’
--- re-building ‘KEGGgraphApp.Rnw’ using Sweave
Loading required package: SPIA
trying URL 'https://rest.kegg.jp/get/hsa05210/kgml'
downloaded 32 KB
--- finished re-building ‘KEGGgraphApp.Rnw’
SUMMARY: processing the following file failed:
‘KEGGgraph.Rnw’
Error: Vignette re-building failed.
Execution halted