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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingleRBook
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* checking for file ‘SingleRBook/DESCRIPTION’ ... OK
* preparing ‘SingleRBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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-3.23-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('SingleRBook'); 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 Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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('SingleRBook'); 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: diagnostics.Rmd
# 1/38
# 2/38 [unnamed-chunk-1]
# 3/38
# 4/38 [unnamed-chunk-2]
# 5/38
# 6/38 [unnamed-chunk-3]
# 7/38
# 8/38 [score-heatmap-grun]
# 9/38
# 10/38 [score-heatmap-grun-donor]
# 11/38
# 12/38 [unnamed-chunk-4]
# 13/38
# 14/38 [unnamed-chunk-5]
# 15/38
# 16/38 [unnamed-chunk-6]
# 17/38
# 18/38 [score-dist-grun]
# 19/38
# 20/38 [unnamed-chunk-7]
# 21/38
# 22/38 [grun-beta-heat]
# 23/38
# 24/38 [unnamed-chunk-8]
# 25/38
# 26/38 [grun-beta-heat-all]
# 27/38
# 28/38 [grun-epsilon-heat]
# Error in `.positive_padded_median()`:
# ! padding < x_len is not TRUE
# Backtrace:
# ▆
# 1. ├─scuttle::summarizeAssayByGroup(mat, config$predictions)
# 2. └─scuttle::summarizeAssayByGroup(mat, config$predictions)
# 3. └─scuttle (local) .local(x, ...)
# 4. └─scuttle:::.summarize_assay(...)
# 5. └─DelayedArray::blockApply(...)
# 6. └─DelayedArray::gridApply(...)
# 7. └─S4Arrays:::bplapply2(...)
# 8. ├─BiocGenerics::lapply(X, FUN, ...)
# 9. └─base::lapply(X, FUN, ...)
# 10. └─DelayedArray (local) FUN(X[[i]], ...)
# 11. └─DelayedArray (local) FUN(viewport, ...)
# 12. └─scuttle (local) FUN(block, ...)
# 13. └─base::lapply(by.group, function(i) rowMedians(x[, i, drop = FALSE]))
# 14. └─scuttle (local) FUN(X[[i]], ...)
# 15. ├─MatrixGenerics::rowMedians(x[, i, drop = FALSE])
# 16. └─SparseArray::rowMedians(x[, i, drop = FALSE])
# 17. └─SparseArray:::.colMedians_SVT_SparseMatrix(...)
# 18. └─base::vapply(...)
# 19. └─SparseArray (local) FUN(X[[i]], ...)
# 20. └─SparseArray:::.padded_median(lv_vals, padding, na.rm = na.rm)
# 21. └─SparseArray:::.positive_padded_median(-x[-pos_idx], padding = nonneg_count)
# 22. └─base::stopifnot(padding < x_len)
#
# Quitting from diagnostics.Rmd:172-177 [grun-epsilon-heat]
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# <error/rlang_error>
# Error in `.positive_padded_median()`:
# ! padding < x_len is not TRUE
# ---
# Backtrace:
# ▆
# 1. ├─scuttle::summarizeAssayByGroup(mat, config$predictions)
# 2. └─scuttle::summarizeAssayByGroup(mat, config$predictions)
# 3. └─scuttle (local) .local(x, ...)
# 4. └─scuttle:::.summarize_assay(...)
# 5. └─DelayedArray::blockApply(...)
# 6. └─DelayedArray::gridApply(...)
# 7. └─S4Arrays:::bplapply2(...)
# 8. ├─BiocGenerics::lapply(X, FUN, ...)
# 9. └─base::lapply(X, FUN, ...)
# 10. └─DelayedArray (local) FUN(X[[i]], ...)
# 11. └─DelayedArray (local) FUN(viewport, ...)
# 12. └─scuttle (local) FUN(block, ...)
# 13. └─base::lapply(by.group, function(i) rowMedians(x[, i, drop = FALSE]))
# 14. └─scuttle (local) FUN(X[[i]], ...)
# 15. ├─MatrixGenerics::rowMedians(x[, i, drop = FALSE])
# 16. └─SparseArray::rowMedians(x[, i, drop = FALSE])
# 17. └─SparseArray:::.colMedians_SVT_SparseMatrix(...)
# 18. └─base::vapply(...)
# 19. └─SparseArray (local) FUN(X[[i]], ...)
# 20. └─SparseArray:::.padded_median(lv_vals, padding, na.rm = na.rm)
# 21. └─SparseArray:::.positive_padded_median(-x[-pos_idx], padding = nonneg_count)
# 22. └─base::stopifnot(padding < x_len)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Execution halted
Error in compileChapter(path) :
failed to compile '~/.cache/rebook/SingleRBook/1.21.0/diagnostics.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