Back to Books build report for BioC 3.14

This page was generated on 2021-10-22 15:00:05 -0400 (Fri, 22 Oct 2021).

BUILD results for OSCA.multisample on nebbiolo2

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Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 6/8HostnameOS / ArchINSTALLBUILD
OSCA.multisample 1.1.0  (landing page)
Aaron Lun
Snapshot Date: 2021-10-22 07:50:01 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/OSCA.multisample
git_branch: master
git_last_commit: e7653c9
git_last_commit_date: 2021-05-19 11:15:53 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  

Summary

Package: OSCA.multisample
Version: 1.1.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.multisample
StartedAt: 2021-10-22 08:01:04 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 09:02:33 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 3689.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.multisample
###
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* 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 4.1.1 (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.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)
# 
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# processing file: using-corrected-values.Rmd
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# Loading required package: SummarizedExperiment
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# Attaching package: 'MatrixGenerics'
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# Loading required package: GenomicRanges
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#     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
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# Loading required package: S4Vectors
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# Loading required package: IRanges
# Loading required package: GenomeInfoDb
# Loading required package: Biobase
# Welcome to Bioconductor
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#     Vignettes contain introductory material; view with
#     'browseVignettes()'. To cite Bioconductor, see
#     'citation("Biobase")', and for packages 'citation("pkgname")'.
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# Quitting from lines 159-162 (using-corrected-values.Rmd) 
# Error: "CD3D" %in% head(demo$Symbol) is not TRUE
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# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.multisample/1.1.0/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