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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.basic
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* checking for file ‘OSCA.basic/DESCRIPTION’ ... OK
* preparing ‘OSCA.basic’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata,
e.g. by using --metadata pagetitle="..." on the command line.
Falling back to 'stub.knit'
--- finished re-building ‘stub.Rmd’
"/home/biocbuild/bbs-3.13-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.basic'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> work.dir <- rebook::bookCache('OSCA.basic'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)
#
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# processing file: normalization.Rmd
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# label: setup (with options)
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# label: unnamed-chunk-2
# Loading required package: SingleCellExperiment
# Loading required package: SummarizedExperiment
# Loading required package: MatrixGenerics
# Loading required package: matrixStats
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# Attaching package: 'MatrixGenerics'
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# The following objects are masked from 'package:matrixStats':
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# colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
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# 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
# Loading required package: parallel
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# Attaching package: 'BiocGenerics'
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# The following objects are masked from 'package:parallel':
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# clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
# clusterExport, clusterMap, parApply, parCapply, parLapply,
# parLapplyLB, parRapply, parSapply, parSapplyLB
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# The following objects are masked from 'package:stats':
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# IQR, mad, sd, var, xtabs
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# The following objects are masked from 'package:base':
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# 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
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# Loading required package: S4Vectors
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# Attaching package: 'S4Vectors'
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# The following objects are masked from 'package:base':
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# I, expand.grid, unname
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# 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")'.
#
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# Attaching package: 'Biobase'
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# The following object is masked from 'package:MatrixGenerics':
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# Loading required package: scuttle
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# label: unnamed-chunk-5
# snapshotDate(): 2021-05-18
# see ?scRNAseq and browseVignettes('scRNAseq') for documentation
# loading from cache
# Quitting from lines 131-135 (normalization.Rmd)
# Error: failed to load resource
# name: EH3102
# title: Richard CD8+ T cell counts
# reason: unknown input format
#
# Execution halted
Error in compileChapter(path) :
failed to compile '~/.cache/rebook/OSCA.basic/1.0.0/normalization.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted