##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.multisample
###
##############################################################################
##############################################################################


* checking for file ‘OSCA.multisample/DESCRIPTION’ ... OK
* preparing ‘OSCA.multisample’:
* 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-3.14-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.multisample'); 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.multisample'); 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)
# 
# 
# processing file: using-corrected-values.Rmd
# 
#   |                                                                            
#   |                                                                      |   0%
#   |                                                                            
#   |..                                                                    |   3%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |....                                                                  |   6%
# label: setup (with options) 
# List of 2
#  $ echo   : logi FALSE
#  $ results: chr "asis"
# 
# 
#   |                                                                            
#   |......                                                                |   8%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |........                                                              |  11%
# label: unnamed-chunk-1 (with options) 
# List of 2
#  $ results: chr "asis"
#  $ echo   : logi FALSE
# 
# 
#   |                                                                            
#   |..........                                                            |  14%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |............                                                          |  17%
# label: unnamed-chunk-2
# 
#   |                                                                            
#   |..............                                                        |  19%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |................                                                      |  22%
# label: unnamed-chunk-3 (with options) 
# List of 2
#  $ results: chr "asis"
#  $ echo   : logi FALSE
# 
# 
#   |                                                                            
#   |..................                                                    |  25%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |...................                                                   |  28%
# label: unnamed-chunk-4
# 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 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
# 
# 
#   |                                                                            
#   |.....................                                                 |  31%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |.......................                                               |  33%
# label: unnamed-chunk-5 (with options) 
# List of 2
#  $ echo: logi FALSE
#  $ eval: logi FALSE
# 
# 
#   |                                                                            
#   |.........................                                             |  36%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |...........................                                           |  39%
# label: pancreas-mnn-delta (with options) 
# List of 2
#  $ fig.asp: num 1
#  $ fig.cap: chr "Distribution of uncorrected expression values for _INS-IGF2_ across the cell types in the Grun and Muraro pancreas datasets."
# 
# Loading required package: SingleCellExperiment
# Loading required package: scuttle
# Loading required package: ggplot2
# 
#   |                                                                            
#   |.............................                                         |  42%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |...............................                                       |  44%
# label: unnamed-chunk-6 (with options) 
# List of 1
#  $ echo: logi FALSE
# 
# 
#   |                                                                            
#   |.................................                                     |  47%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |...................................                                   |  50%
# label: pancreas-mnn-delta2 (with options) 
# List of 2
#  $ fig.asp: num 1
#  $ fig.cap: chr "Distribution of MNN-corrected expression values for _INS-IGF2_ across the cell types in the Grun and Muraro pancreas datasets."
# 
# 
#   |                                                                            
#   |.....................................                                 |  53%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |.......................................                               |  56%
# label: unnamed-chunk-7 (with options) 
# List of 2
#  $ results: chr "asis"
#  $ echo   : logi FALSE
# 
# 
#   |                                                                            
#   |.........................................                             |  58%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |...........................................                           |  61%
# label: pbmc-marker-blocked (with options) 
# List of 3
#  $ fig.width : num 10
#  $ fig.height: num 8
#  $ fig.cap   : chr "Distributions of uncorrected log-expression values for _CD8B_ and _CD3D_ within each cluster in each batch of t"| __truncated__
# 
# Loading required package: HDF5Array
# Loading required package: DelayedArray
# Loading required package: Matrix
# 
# Attaching package: 'Matrix'
# 
# The following object is masked from 'package:S4Vectors':
# 
#     expand
# 
# 
# Attaching package: 'DelayedArray'
# 
# The following objects are masked from 'package:base':
# 
#     aperm, apply, rowsum, scale, sweep
# 
# Loading required package: rhdf5
# 
# Attaching package: 'HDF5Array'
# 
# The following object is masked from 'package:rhdf5':
# 
#     h5ls
# 
# 
#   |                                                                            
#   |.............................................                         |  64%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |...............................................                       |  67%
# label: unnamed-chunk-8 (with options) 
# List of 1
#  $ echo: logi FALSE
# 
# Quitting from lines 159-162 (using-corrected-values.Rmd) 
# Error: "CD3D" %in% head(demo$Symbol) is not TRUE
# 
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.multisample/1.2.2/using-corrected-values.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