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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data PloGO2
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* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* preparing ‘PloGO2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘PloGO2_vignette.Rnw’ using Sweave
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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
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: GOstats
Loading required package: Category
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Loading required package: graph
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’
Attaching package: ‘GOstats’
The following object is masked from ‘package:AnnotationDbi’:
makeGOGraph
No encoding supplied: defaulting to UTF-8.
Error: processing vignette 'PloGO2_vignette.Rnw' failed with diagnostics:
unable to run pdflatex on 'PloGO2_vignette.tex'
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.8 \textwidth
=6.2in^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘PloGO2_vignette.Rnw’
--- re-building ‘PloGO2_with_WGNCA_vignette.Rnw’ using Sweave
Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Attaching package: ‘WGCNA’
The following object is masked from ‘package:IRanges’:
cor
The following object is masked from ‘package:S4Vectors’:
cor
The following object is masked from ‘package:stats’:
cor
dev.new(): using pdf(file="Rplots1.pdf")
Error: processing vignette 'PloGO2_with_WGNCA_vignette.Rnw' failed with diagnostics:
unable to run pdflatex on 'PloGO2_with_WGNCA_vignette.tex'
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.8 \textwidth
=6.2in^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘PloGO2_with_WGNCA_vignette.Rnw’
SUMMARY: processing the following files failed:
‘PloGO2_vignette.Rnw’
‘PloGO2_with_WGNCA_vignette.Rnw’
Error: Vignette re-building failed.
Execution halted