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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Hiiragi2013
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* checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK
* preparing ‘Hiiragi2013’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Hiiragi2013.Rnw’ using Sweave
Loading required package: affy
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: 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: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
Loading required package: lattice
Attaching package: ‘lattice’
The following object is masked from ‘package:boot’:
melanoma
Loading required package: annotate
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: XML
Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:IRanges’:
space
The following object is masked from ‘package:S4Vectors’:
space
The following object is masked from ‘package:stats’:
lowess
Loading required package: gtools
Attaching package: ‘gtools’
The following objects are masked from ‘package:boot’:
inv.logit, logit
Loading required package: KEGGREST
Loading required package: MASS
Attaching package: ‘MASS’
The following object is masked from ‘package:AnnotationDbi’:
select
The following object is masked from ‘package:genefilter’:
area
Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db
Loading required package: RColorBrewer
Loading required package: xtable
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘mouse4302cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘mouse4302cdf’
Error: processing vignette 'Hiiragi2013.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Hiiragi2013.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `Gray'.
See the xcolor package documentation for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.1 library("
affy")
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Hiiragi2013.Rnw’
SUMMARY: processing the following file failed:
‘Hiiragi2013.Rnw’
Error: Vignette re-building failed.
Execution halted