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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dorothea
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* checking for file ‘dorothea/DESCRIPTION’ ... OK
* preparing ‘dorothea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bulk_vignette.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
--- finished re-building ‘bulk_vignette.Rmd’
--- re-building ‘single_cell_vignette.Rmd’ using rmarkdown
Attaching SeuratObject
Performing log-normalization
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Performing log-normalization
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Calculating gene variances
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Calculating feature variances of standardized and clipped values
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Centering and scaling data matrix
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Quitting from lines 146-160 (single_cell_vignette.Rmd)
Error: processing vignette 'single_cell_vignette.Rmd' failed with diagnostics:
invalid class "Graph" object: superclass "Mnumeric" not defined in the environment of the object's class
--- failed re-building ‘single_cell_vignette.Rmd’
SUMMARY: processing the following file failed:
‘single_cell_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted