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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 SummarizedBenchmark
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* checking for file ‘SummarizedBenchmark/DESCRIPTION’ ... OK
* preparing ‘SummarizedBenchmark’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CaseStudy-RNAseqQuantification.Rmd’ using rmarkdown
Loading required package: tidyr
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
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, 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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:tidyr':
expand
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: UpSetR
Loading required package: rlang
Attaching package: 'rlang'
The following object is masked from 'package:Biobase':
exprs
Loading required package: stringr
Loading required package: BiocParallel
Loading required package: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.10
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:matrixStats':
count
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: digest
Loading required package: sessioninfo
Loading required package: crayon
Attaching package: 'crayon'
The following object is masked from 'package:ggplot2':
%+%
The following object is masked from 'package:rlang':
chr
Loading required package: tibble
--- finished re-building ‘CaseStudy-RNAseqQuantification.Rmd’
--- re-building ‘CaseStudy-SingleCellSimulation.Rmd’ using rmarkdown
Attaching package: 'magrittr'
The following object is masked from 'package:rlang':
set_names
The following object is masked from 'package:GenomicRanges':
subtract
The following object is masked from 'package:tidyr':
extract
Quitting from lines 47-54 (CaseStudy-SingleCellSimulation.Rmd)
Error: processing vignette 'CaseStudy-SingleCellSimulation.Rmd' failed with diagnostics:
there is no package called 'splatter'
--- failed re-building ‘CaseStudy-SingleCellSimulation.Rmd’
--- re-building ‘Feature-ErrorHandling.Rmd’ using rmarkdown
--- finished re-building ‘Feature-ErrorHandling.Rmd’
--- re-building ‘Feature-Iterative.Rmd’ using rmarkdown
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Quitting from lines 43-57 (Feature-Iterative.Rmd)
Error: processing vignette 'Feature-Iterative.Rmd' failed with diagnostics:
there is no package called 'edgeR'
--- failed re-building ‘Feature-Iterative.Rmd’
--- re-building ‘Feature-Parallel.Rmd’ using rmarkdown
Quitting from lines 41-55 (Feature-Parallel.Rmd)
Error: processing vignette 'Feature-Parallel.Rmd' failed with diagnostics:
there is no package called 'edgeR'
--- failed re-building ‘Feature-Parallel.Rmd’
--- re-building ‘SummarizedBenchmark-ClassDetails.Rmd’ using rmarkdown
Attaching package: 'iCOBRA'
The following objects are masked from 'package:GenomicRanges':
score, score<-
The following objects are masked from 'package:BiocGenerics':
score, score<-
--- finished re-building ‘SummarizedBenchmark-ClassDetails.Rmd’
--- re-building ‘SummarizedBenchmark-FullCaseStudy.Rmd’ using rmarkdown
Quitting from lines 32-39 (SummarizedBenchmark-FullCaseStudy.Rmd)
Error: processing vignette 'SummarizedBenchmark-FullCaseStudy.Rmd' failed with diagnostics:
there is no package called 'edgeR'
--- failed re-building ‘SummarizedBenchmark-FullCaseStudy.Rmd’
--- re-building ‘SummarizedBenchmark-Introduction.Rmd’ using rmarkdown
Found already estimated performance metrics, replacing these
--- finished re-building ‘SummarizedBenchmark-Introduction.Rmd’
SUMMARY: processing the following files failed:
‘CaseStudy-SingleCellSimulation.Rmd’ ‘Feature-Iterative.Rmd’
‘Feature-Parallel.Rmd’ ‘SummarizedBenchmark-FullCaseStudy.Rmd’
Error: Vignette re-building failed.
Execution halted
