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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 MineICA
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* checking for file ‘MineICA/DESCRIPTION’ ... OK
* preparing ‘MineICA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MineICA.Rnw’ using Sweave
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:plyr’:
rename
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findMatches
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I, expand.grid, unname
Attaching package: ‘IRanges’
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desc
Loading required package: Matrix
Attaching package: ‘Matrix’
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expand
Loading required package: graph
Attaching package: ‘graph’
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join
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’
Attaching package: ‘GOstats’
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makeGOGraph
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Attaching package: ‘igraph’
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degree, edges, intersection, union
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union
The following object is masked from ‘package:S4Vectors’:
union
The following objects are masked from ‘package:BiocGenerics’:
normalize, path, union
The following objects are masked from ‘package:stats’:
decompose, spectrum
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union
Loading required package: grid
Attaching package: ‘Rgraphviz’
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from, to
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from, to
Loading required package: XML
Attaching package: ‘XML’
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addNode
Attaching package: ‘annotate’
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toFile
Attaching package: ‘gtools’
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permute
Loading required package: Hmisc
Attaching package: ‘Hmisc’
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contents
The following objects are masked from ‘package:xtable’:
label, label<-
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is.discrete, summarize
The following object is masked from ‘package:Biobase’:
contents
The following objects are masked from ‘package:base’:
format.pval, units
Loading required package: fastICA
Loading required package: JADE
Number of selected genes is 10000
Max IQR is 0.89
Loading required package: org.Hs.eg.db
..Features annotation with package hgu133a.db..
...Annotation into SYMBOL..
The number of probe sets not associated with a SYMBOL ID is 1301
The remaining number of probe sets is 8699
The number of genes annotated by several features is 1548
Warning: executing %dopar% sequentially: no parallel backend registered
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Warning: The `axis.ticks.margin` argument of `theme()` is deprecated as of ggplot2
2.0.0.
ℹ Please set `margin` property of `axis.text` instead
ℹ The deprecated feature was likely used in the MineICA package.
Please report the issue to the authors.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
`geom_smooth()` using formula = 'y ~ x'
Error: processing vignette 'MineICA.Rnw' failed with diagnostics:
unable to run pdflatex on 'MineICA.tex'
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.23 \usepackage
{subfig}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘MineICA.Rnw’
SUMMARY: processing the following file failed:
‘MineICA.Rnw’
Error: Vignette re-building failed.
Execution halted