##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 KEGGgraph
###
##############################################################################
##############################################################################
* 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
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, saveRDS, setdiff, table,
tapply, union, 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
trying URL 'https://rest.kegg.jp/get/hsa04010/kgml'
Warning in download.file(needdown[i], tmps[i], method = downloadmethod, :
cannot open URL 'https://rest.kegg.jp/get/hsa04010/kgml': HTTP status was '404 Not Found'
Error: processing vignette 'KEGGgraph.Rnw' failed with diagnostics:
chunk 21 (label = mapk14expand)
Error in download.file(needdown[i], tmps[i], method = downloadmethod, :
cannot open URL 'https://rest.kegg.jp/get/hsa04010/kgml'
--- 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