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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 simplifyEnrichment
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* checking for file ‘simplifyEnrichment/DESCRIPTION’ ... OK
* preparing ‘simplifyEnrichment’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘interactive.Rmd’ using rmarkdown
--- finished re-building ‘interactive.Rmd’
--- re-building ‘simplifyEnrichment.Rmd’ using rmarkdown
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, 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: grid
========================================
simplifyEnrichment version 1.7.1
Bioconductor page: https://bioconductor.org/packages/simplifyEnrichment/
Github page: https://github.com/jokergoo/simplifyEnrichment
Documentation: https://jokergoo.github.io/simplifyEnrichment/
Examples: https://simplifyenrichment.github.io/
This message can be suppressed by:
suppressPackageStartupMessages(library(simplifyEnrichment))
========================================
Cluster 500 terms by 'binary_cut'... 19 clusters, used 1.844182 secs.
Perform keywords enrichment for 11 GO lists...
Cluster 500 terms by 'binary_cut'... 19 clusters, used 2.954298 secs.
Cluster 500 terms by 'kmeans'... 15 clusters, used 8.992925 secs.
Cluster 500 terms by 'pam'... 5 clusters, used 1.1171 mins.
Cluster 500 terms by 'dynamicTreeCut'... 60 clusters, used 0.4930842 secs.
Cluster 500 terms by 'apcluster'... 41 clusters, used 2.956976 secs.
Cluster 500 terms by 'hdbscan'... 14 clusters, used 0.530185 secs.
Cluster 500 terms by 'fast_greedy'... 6 clusters, used 0.48649 secs.
Cluster 500 terms by 'louvain'... 6 clusters, used 0.2577581 secs.
Cluster 500 terms by 'walktrap'... 6 clusters, used 0.937134 secs.
Cluster 500 terms by 'MCL'... 6 clusters, used 3.162281 secs.
Cluster 500 terms by 'binary_cut'... 19 clusters, used 1.889515 secs.
Cluster 500 terms by 'kmeans'... 20 clusters, used 6.246307 secs.
Cluster 500 terms by 'pam'... 5 clusters, used 32.58266 secs.
Cluster 500 terms by 'dynamicTreeCut'... 60 clusters, used 0.192816 secs.
Cluster 500 terms by 'apcluster'... 41 clusters, used 2.085332 secs.
Cluster 500 terms by 'hdbscan'... 14 clusters, used 0.2607751 secs.
Cluster 500 terms by 'fast_greedy'... 6 clusters, used 0.2312109 secs.
Cluster 500 terms by 'louvain'... 6 clusters, used 0.103781 secs.
Cluster 500 terms by 'walktrap'... 6 clusters, used 0.578825 secs.
Cluster 500 terms by 'MCL'... 6 clusters, used 2.254529 secs.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <89>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <a5>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <89>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <a5>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <89>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <a5>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <89>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <a5>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <89>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <a5>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
conversion failure on 'Large clusters (size ≥ 5)' in 'mbcsToSbcs': dot substituted for <89>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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Quitting from lines 287-300 (simplifyEnrichment.Rmd)
Error: processing vignette 'simplifyEnrichment.Rmd' failed with diagnostics:
there is no package called 'cola'
--- failed re-building ‘simplifyEnrichment.Rmd’
--- re-building ‘word_cloud_anno.Rmd’ using rmarkdown
Loading required package: NLP
Attaching package: 'NLP'
The following object is masked from 'package:BiocGenerics':
annotation
========================================
ComplexHeatmap version 2.13.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
The new InteractiveComplexHeatmap package can directly export static
complex heatmaps into an interactive Shiny app with zero effort. Have a try!
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
========================================
circlize version 0.4.15
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/
If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
in R. Bioinformatics 2014.
This message can be suppressed by:
suppressPackageStartupMessages(library(circlize))
========================================
Perform keywords enrichment for 4 GO lists...
--- finished re-building ‘word_cloud_anno.Rmd’
SUMMARY: processing the following file failed:
‘simplifyEnrichment.Rmd’
Error: Vignette re-building failed.
Execution halted
