Back to Books build report for BioC 3.14

This page was generated on 2022-04-08 14:00:04 -0400 (Fri, 08 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4322
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BUILD results for OSCA.multisample on nebbiolo2


To the developers/maintainers of the OSCA.multisample package:
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 1.2.2  (landing page)
Aaron Lun
Snapshot Date: 2022-04-08 06:45:01 -0400 (Fri, 08 Apr 2022)
git_url: https://git.bioconductor.org/packages/OSCA.multisample
git_branch: RELEASE_3_14
git_last_commit: e8ceb31
git_last_commit_date: 2022-01-20 23:54:25 -0400 (Thu, 20 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  

Summary

Package: OSCA.multisample
Version: 1.2.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.multisample
StartedAt: 2022-04-08 07:01:03 -0400 (Fri, 08 Apr 2022)
EndedAt: 2022-04-08 08:03:02 -0400 (Fri, 08 Apr 2022)
EllapsedTime: 3718.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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
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# label: unnamed-chunk-4
# Loading required package: SummarizedExperiment
# Loading required package: MatrixGenerics
# Loading required package: matrixStats
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# Attaching package: 'MatrixGenerics'
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#     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
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#     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,
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# Loading required package: GenomicRanges
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# Attaching package: 'BiocGenerics'
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#     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
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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/1.2.2/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